Time After Time
by ShaViva
Summary: "We already did," Sheppard almost growled. When a familiar face arrives with a warning Sheppard is forced to push his unique connection with Atlantis to the limit. Third in my Sheplantis series, follows on from Feelin' Hot Hot Hot and You Belong to Me.
1. Find what you were looking for?

**Time After Time**

Author: ShaViva

Rating: K+

Content Warning: Minor character distress is pretty much it.

Season: Season 3 - Carson's still around so sometime before Sunday but after 'The Return Part 2' because they have a ZPM.

Summary: '"We already did," Sheppard almost growled.' When a familiar face arrives with a warning Sheppard is forced to push his unique connection with Atlantis to the limit. Follows on from 'You Belong to Me' and "Feelin' Hot Hot Hot'.

Classifications: Adventure, Drama, Team Friendship, Shep Whump, Sheplantis

Pairings: None

Spoilers for: a few for McKay and Mrs Miller plus very minor (blink and you'd miss it) ones for The Defiant One, The Siege Pt 2, The Return Pt 1 & 2, First Strike, and the SG1 episode Point of View.

Disclaimer: The Stargate characters, storylines, etc aren't mine – I'm just playing with them for my own, and hopefully _your_ enjoyment. I am unfortunately not associated in any way with the creators, owners, or producers of Stargate or any of its media franchises - if I was we'd be seeing SGA on TV for many more years to come! All publicly recognizable characters, settings, equipment, etc are the property of whoever owns them. Any original characters and plot and anything else I made up are the property of me, the author. No copyright infringement is intended.

Copyright (c) 2008 ShaViva

**Authors Note:**

This story is the third in a trilogy. Feelin' Hot Hot Hot was the first story, followed closely by the second story You Belong to Me. The second one was set before The Return and this one is after it so a month or so has gone by. This probably makes sense without having read the other two stories but ... it would probably enhance it if you did read them as there are a few 'spoilers' for those stories here.

I was gonna hold off starting the posts on this one but picking over it is distracting me from working on FJS4 so here it is. I can't promise a daily post ... I tend to get caught up writing Shep/Sab ... but I'll do my best!

And now, on with the story ...

**Chapter 1: Find what you were looking for?**

Lt Colonel John Sheppard groaned at the pain of a Replicator hand being removed from his forehead. It wasn't a new experience but unfortunately it still hurt like a son of a bitch. He didn't even know where he was ... one Ancient holding cell looked much the same as another and he had no recollection of being taken there.

"Find what you were looking for?" he quipped, doing a pretty good job of hiding the less than positive effect the mind probe had had on him.

"Your mind is strong," the Replicator almost complimented. "We have most of what we require but ... there is still much we could learn from you."

"Well could you hurry it up? I've got things to do and your hospitality isn't exactly five star," Sheppard joked, trying not to worry over what he might have already given away. They really needed a defence against this kind of thing!

"We were going to give you time to rest but ...," without saying anything further the Replicator slid it's hand once more inside Sheppard's head ... inside his mind.

Sheppard groaned again, retaining enough of his true self this time to realise he wasn't really back on Atlantis. He tried to resist but couldn't, watching helplessly as the Replicator riffled through his memories.

oOo

"Anything?" Ronon impatiently looked over Rodney's shoulder at the small data pad in his hand. The rest of Team Sheppard were hidden behind thick trees at the edge of a clearing ... keeping watch on a small building located on the other side.

"If you'd stop breathing down my neck and asking every five minutes if I have anything this would go a lot faster!" Rodney complained.

"I thought you altered the life signs detector to distinguish someone with the Ancestors gene," Ronon said impatiently. "How come you're not picking up Sheppard's signal?"

"I did but it's not as simple as just following the little flashing arrow!" Rodney protested. "I still need to fine tune the calibration and boost the strength so we can scan inside the facility."

"Ronon, let Rodney finish his work," Teyla admonished. "We have already been separated from Colonel Sheppard for several hours. We need to hurry."

"I don't know about either of you but I'm getting tired of every rumour we follow up turning out to be a trap," Rodney multitasked his complaints with rapid button pressing on the Ancient scanner as he hurried to complete his work. "For once it'd be nice to go on one of these exploration missions and actually find an Ancient outpost brimming with everything promised!"

"That'd make for a nice change," Ronon agreed.

"What I don't get is why the Replicators stunned us all at the Gate but only took Sheppard," Rodney continued. "Why go to all the trouble of luring us here and then leave the three of us behind? It doesn't make sense."

"It _is_ different from what we have seen previously with the Replicators," Teyla agreed.

"They want something they think only Sheppard has," Ronon deduced. "or –."

"I've got something," Rodney interrupted to announce triumphantly. "One ATA life sign located ... inside there," he pointed towards the building.

Ronon moved straight into action, sprinting across the clearing, blaster poised ready in front of him. Slamming his back against the wall next to the door he waited a few moments to see if he'd been detected before motioning the others to join him. Teyla moved with her usual silent grace, followed closely by Rodney who was somewhat less graceful and a lot less quiet.

Dropping to one knee in front of the door Rodney quickly accessed the control panel, crossed a few crystals, and was rewarded with the sound of the door swishing open.

"Me first," Ronon put a hand on Rodney's shoulder to hold him back, taking a few steps into the corridor revealed. After getting another all clear the team progressed down the corridor and into the facility. Everything looked exactly as they expected ... the decor very similar to Atlantis and the other Ancient outposts they'd been to.

"That way," Rodney pointed to another corridor heading right. They moved stealthily towards Sheppard's life sign, all the while expecting to be confronted at any moment. The interior was strangely silent ... and strangely empty.

"Are you picking up anything else on that scanner of yours?" Ronon whispered, clearly disturbed by the lack of opposing force they'd encountered so far.

"Hang on," Rodney pressed a few buttons, switching the scanner back to it's normal mode. He frowned in confusion when the results appeared. "If I'm reading this right Sheppard is the only signal in the building – human or Replicator."

"We must hurry," Teyla said again, urging the others to keep moving.

Rodney guided them through the building until they reached a closed door. "He's in there," Rodney hesitated for a moment, not sure he really wanted to open the door if it turned out Sheppard was lying badly injured on the other side.

"Open it," Ronon growled, pacing impatiently.

"I'm on it," Rodney was already pulling off the door control cover. "I like how you just assume I can open any door ... anywhere!" he complained.

"Now would not be the time to prove him wrong," Teyla said sternly.

Rodney worked his usual magic quickly ... when the door swished open a few seconds later it revealed a standard holding cell much like the ones back on Atlantis. John was stretched out on the floor ... strangely the cell itself was already open.

"Sheppard!" Rodney rushed into the opening, dropping down beside his fallen friend. On the outside he looked unharmed but the fact he was unconscious meant _something_ had been done to him.

"John," Teyla put a hand to Sheppard's shoulder and shook him gently.

Sheppard's eyelids flickered, his face moving into a frown as consciousness returned without immediately informing him of his current situation. He groaned weakly, opening his eyes fully before closing them again. "Crap," he muttered, raising a hand and squeezing his forehead tightly. Opening his eyes again he looked at Teyla. "What happened?"

"We had hoped that you would be able to tell us," Teyla admitted.

"The Replicators," Sheppard winced as memory started to return. "They did the whole mind probe thing on me ... a couple of times actually. That's the last thing I remember. What happened to you guys?"

"They stunned us too but did not take us captive," Teyla reported, helping John to sit up slowly.

"Your popularity seems to have extended to the Replicators now – they only wanted you," Rodney's tone seemed to suggest that somehow Sheppard was to blame for that.

"It wasn't my fault!" he protested, the raised tone causing him to grimace in pain.

"Headache?" Rodney asked curiously.

"Yeah," Sheppard admitted. "Those mind probes never get any easier do they?"

"What were they looking for?" Ronon asked seriously, looking at Sheppard expectantly.

"Ah ... I'm not sure," John admitted. "From what I can recall it was all stuff about Atlantis."

"Gate addresses?" Rodney asked worriedly.

"I don't think so ... that's the strange thing," Sheppard admitted. "It was nothing like that ... the last probe was just everyday stuff plus a few titbits of things that have happened over the past couple of months."

"That _is_ odd," Teyla frowned, "and most unlike their usual behaviour."

"They just left?" Ronon quizzed Sheppard, urging him to remember as much as possible.

"I guess," Sheppard agreed. "I was unconscious at the time ... certainly nothing I did _made_ them leave."

"This is bad," Rodney muttered sickly.

"How so?" Ronon asked.

"They're planning something," Rodney pointed out, "and the fact that they let Sheppard go means they probably got exactly what they needed to put their plan into action."

"You're right," Sheppard pulled himself up, stumbling slightly before standing tall. "We need to get back to Atlantis ... right now."


	2. Leave no one behind Major

**Chapter 2: Leave no one behind Major**

Returning to Atlantis was an anticlimax. Nothing was wrong - in fact there had been no contact from anyone, let alone the Replicators, the whole time Team Sheppard had been off world.

"Perhaps they did not find what they were after as we assumed they had," Teyla suggested at the end of the debriefing with Doctor Weir.

"Or we interrupted them before they could get everything," Rodney added. "I was monitoring that place and I didn't pick up anything - I can't see how they could have gotten off that planet undetected before we got there."

"Self destruct?" Ronon suggested.

"It's possible," Rodney agreed. "Might be a way to protect the broader objective ... give them a chance to try again in the future. It wouldn't be the first time we've seen individuals sacrificed for the greater good."

"So we just ignore this one?" Elizabeth glanced from person to person with an expectant look.

"We keep the base on alert for now," Sheppard decided. "Warn the off world teams to be very careful about rumours ... send MALPs for any planets with some degree of uncertainty, even if we've been there before. Beyond that there's nothing much we _can_ do."

"Sheppard's right," Rodney agreed. "Zelenka and I have checked and there's absolutely no evidence suggesting an immediate problem. We can try to track any Replicator activity but ...,"

"We're not likely to find anything useful," Elizabeth finished. "Very well. Implement those measures Colonel ... let's hope we don't have reason to need them."

Atlantis remained on alert for a time but eventually the incident was religated to the category of near miss. Everyone relaxed in the knowledge that things were back to business as usual.

oOo

"How are things with Atlantis these days?" Rodney asked Sheppard one day about a month after the Replicator incident. They, Ronon and Teyla were in the commissary but business was light so there was little chance anyone would overheard them.

"Um ... good I guess," Sheppard replied with a frown. "Why?"

"No reason," Rodney admitted easily. "I was just thinking it's been a while since we've run into any problems requiring that extra edge. You've been less than receptive to advancing any of my research projects lately and I was just wondering. Do you still ... you know ... talk to her?"

"I check in every now and then," Sheppard admitted. "We're not having daily conversations or anything but she knows I'm here. It's not like I can get away from the hum ... unless I'm off world."

"I never thought of it like that," Rodney frowned, clearly thinking about it now. "Isn't that annoying?"

"No more than your constant chatter," Sheppard smiled when Rodney humpfed at the insult. "You get used to it ... like a dripping tap or a clock ticking."

"I never get used to stuff like that," Rodney shared. "In fact when I was in hospital a few years back I made them take down all the clocks. Couldn't sleep for all the noise."

"Then it's lucky you're not the one connected to the city, isn't it?" Sheppard's tone was a clear message that he'd prefer the topic of conversation to change ... as usual Rodney was completely oblivious to anything but his own curiosity.

"So it would have been a relief then, that time we spent back on Earth?" Rodney looked at Sheppard in surprise. "You never said anything about missing the city while the Ancients were in residence."

"_Rodney_," Teyla took pity on John, drawing attention to herself in an effort to head him off. "Do we have any new leads on ZPMs?"

Rodney shifted topic instantly, happy to regale Teyla with a long and involved story about how only his methods for searching the Ancient database would likely bear fruit in that area. Although they now had one fully charged ZPM courtesy of the Tria Rodney still held out for the elusive dream of a fully powered Atlantis. Teyla listened with half an ear, nodding a gracious acknowledgement to Sheppard's grateful smile.

John was still in two minds about his time away from the city during the return of the Ancients. Part of him – mostly his suddenly headache free head – had welcomed the respite from the pressure of being constantly linked to Atlantis. Even off world he didn't completely escape, despite what he'd said to Rodney. He couldn't help but tune in to any Ancient technology with a moderate level of strength to it.

But a larger part of him _had_ been bothered by the separation – he'd felt like part of himself was missing, like he was constantly looking for that greeting that never came. He'd ended up feeling detached from himself and everyone else because he didn't have the city humming away in the background to keep him in the here and now. It had scared him ... realising how dependant he'd become on having Atlantis grounding him and demanding his focus.

Once he'd returned the renewed connection, the sharpening of his perceptions - everything that made him unique to the city - had rushed through him to the point of overwhelming him. Sheppard had overcompensated by trying to keep a distance between himself and Atlantis. As a result he'd lost some of the comfort zone he'd worked to achieve after Aperio ... and had yet to get it back.

Cursing Rodney for getting his mind thinking in that direction Sheppard made a conscious effort to push it to the background where it belonged. He'd think about how to fix it ... later.

oOo

"Colonel Sheppard, please report to the Control Room."

John looked up from his desk, happy for the interruption. Paper work was a necessary evil – even so far away from Earth it seemed the pencil pushers held the power to command reports ... about every minor detail.

"On my way," Sheppard threw down his pen, striding purposefully from his office.

"Colonel," Doctor Weir welcomed his presence, drawing his attention to one of the screens, currently displaying the image of Sergeant Cooper, second ranked officer on Major Lorne's team. "Colonel Sheppard's here Sergeant – go ahead."

"We've got a little situation Sir," Cooper reported in from M4R 379. "When we got here the village leader insisted on meeting with Major Lorne by himself. There didn't seem to be any reason not to – we've met with these people in the past with no problems. Only thing is today ... well they're refusing to let Major Lorne leave."

"What?" Sheppard demanded with a confused frown.

"We haven't seen the Major since he went into the council room," Cooper explained. "The leader insists on speaking with you Sir – said he won't let Major Lorne go unless you come here."

"Colonel Sheppard specifically or just the person in charge?" Elizabeth asked.

"He asked for Colonel Sheppard personally Ma'am," Cooper confirmed.

"Give us a few minutes," Sheppard replied grimly. "We'll radio you once we're through the Gate."

"Yes Sir," Cooper nodded moments before the wormhole shut down.

"This is a friendly planet right?" Sheppard turned to Elizabeth questioningly.

"It is," Elizabeth agreed. "We've completed a number of successful trade negotiations in the past ... including more than one led by Major Lorne."

"So what went wrong today," Sheppard mused, "and how did they even know to ask for me?"

"Get your team ready," Elizabeth replied. "Go and find out ... and Colonel?" John looked at her expectantly. "Be careful – this could very well be a trap."

"Seems more than likely," Sheppard agreed, implicitly reassuring Elizabeth that he'd treat the situation with caution.

oOo

"Tell me again why it was necessary for me to be here?" Rodney complained, trudging down the forest path behind Sheppard. "I was running an important experiment you know – one that could prove invaluable. Surely that's a higher priority than communing with a bunch of primitive people who've only just discovered the wheel!"

"Primitive people who have Major Lorne hostage," Sheppard reminded him. "Stop complaining Rodney and start scanning ... look for anything out of place."

"Fine," Rodney muttered under his breath, holding out his Ancient scanner industriously. "Even though this is like using a micro surgeon to remove a splinter."

"That _would_ be funny," Sheppard pointed out, "except haven't you been to Carson on more than one occasion for exactly that?"

Ronon and Teyla both laughed, well acquainted with Rodney's hypochondria.

"Hey, one of those splinters penetrated into the subcutaneous layer," Rodney defended himself. "My skin is very sensitive to – ," Rodney broke off suddenly, frowning down at his data pad in confusion. "We've had survey teams here before right?"

"More than once," Sheppard confirmed.

"And they never found any evidence of Ancient technology?" Rodney persisted.

"No – why?" Sheppard looked at Rodney, his expression demanding an explanation.

"Because I'm picking up an energy reading," Rodney revealed. "Admittedly it's extremely faint so maybe those teams missed it ... but there is definitely something here that's giving off an Ancient signature."

"What is it?" Ronon asked curiously.

"Did I not just say 'extremely faint'?" Rodney replied impatiently. "We'll need to get much closer before I can say for sure."

"Okay," Sheppard paused to think about the options. "You and Ronon follow that up ... Teyla and I'll proceed to the village to negotiate for Lorne's release."

"There's no hurry," Rodney said, looking at Ronon somewhat reluctantly. The Satedan was less than patient when it came to Rodney's work – something he'd like to avoid while on an alien planet with no one else around. "We could ... you know ... wait until the whole team can go."

"You just finished telling me how your talents are wasted on a rescue mission," Sheppard reminded him. "Go with Ronon – I'm sure he'll be cooperative." Sheppard made eye contact with his friend, silently asking him to humour Rodney.

"Be careful," Ronon cautioned, reluctant himself to separate from the rest of the team when the situation was still unknown.

"You too – maintain radio silence until we contact you," Sheppard returned. "And don't let Rodney turn anything on."

Sheppard smiled as the two men headed off through the trees, Rodney's muttered complaints that Sheppard was usually the one randomly switching on Ancient devices trailing behind them. Turning to Teyla he raised an eyebrow in query. Teyla nodded and the two of them continued on towards the village.

oOo

"Major Lorne is free to leave any time," the leader of the village, a man Sheppard had dubbed 'Tom' because his real name was too hard to pronounce, announced. The village had turned out to be just as primitive as Rodney had theorised, putting John in mind of the 'peasants' village on the Tower planet ... not an inspiring thought and he put in a fervent request to the powers that be for the absence of any administrators bent on beytrayal and domination.

"You're just gonna let Lorne go?" Sheppard frowned in confusion. "No hostage demands?"

"The Major was never a hostage," Tom replied. "He was our honoured guest until such time as you were able to visit us. Your presence here was most desired by everyone in the village."

"And why was that again?" Sheppard persisted, puzzled about the man's motives.

"Having a direct descendant of the Ancestors visit our village is a great honour, said to bestow prosperity and happiness upon any who live here," Tom revealed. "When we heard that _you_ were such a descendant we resolved immediately to make that happen."

"You could have just invited me," Sheppard pointed out in exasperation, trying not to show his embarrassment at the man's obvious admiration and overly flowery speech.

"We did," Tom didn't excuse his methods. "We asked Major Lorne to stay to ensure that you would accept our invitation. My people will enjoy much good fortune from this but still ... I hope my actions today have not damaged our continuing relationship with your people."

"From where did you hear of the Colonel's connection to the Ancients?" Teyla asked curiously.

"Off-worlders come to trade here regularly," Tom explained. "There was one just over a week ago who told stories of the Colonel's links to the Ancestors. It is quite common for visitors to share such stories – although this was the first time we had heard any about our Lantean friends."

"We understand your motives," Teyla spoke before Sheppard could say anything. "I am sure Doctor Weir will understand your village legends and excuse this incident ... as long as you agree to refrain from such action in the future."

"Of course," Tom agreed readily, turning to one of his colleagues purposefully. "Have Major Lorne escorted here immediately."

Tom and Teyla spoke of inconsequential things while they waited for Lorne to appear. Sheppard sat in silent contemplation, hardly listening to the conversation going on around him. On the surface this all seemed up front and on the level but ... something didn't gel for him, he just couldn't put a finger on what it was.

"Sir," Major Lorne entered the room with a somewhat apologetic expression, looking none the worse for wear. "Thanks for turning up."

"Leave no one behind Major," Sheppard said flippantly, "even the supposedly honoured guests."

"Yes Sir," Major Lorne's behaviour confirmed without further explanation that he had indeed been treated properly.

"Ready to head home?" Sheppard quizzed, turning back to Tom with a raised eyebrow. "I assume me just being here is all you were after?"

"It was," Tom agreed. "Thank you again for coming so promptly ... we would welcome you back should you choose to return in the future."

"Ah ... I'm not really partial to being the subject of village legend," Sheppard quipped. "Not that your home isn't nice and all."

"We understand," Tom smiled pleasantly, obviously not bothered by Sheppard's less than graceful response to his invitation.

"Before we go there was one other thing," Sheppard's tone suggested nothing more than a minor matter. "Are there any Ancient structures or ruins near here?"

"Not that I have seen," Tom replied. "The records do speak of a time when the Ancestors visited often but that was many thousands of years ago."

"Would you mind if we stayed for a while, checked things out?" Sheppard asked.

"Of course not ... stay as long as you like," Tom agreed. "I hope you find that which you seek."

Taking their leave Sheppard, Teyla and Major Lorne headed back through the forest towards the place where they'd separated from Rodney and Ronon.

"Rodney, have you got anything yet?" Sheppard used the radios to get a progress report.

"You've got Lorne?" Rodney didn't answer the question directly but his excitement was a resounding yes.

"We have," Sheppard agreed. "Didn't even have to give them anything."

"While I'm sure it's a fascinating story," Rodney said impatiently, "it'll have to wait – can you make your way to our position?"

"You found something," Sheppard stated.

"To be honest I don't know," Rodney admitted. "I need you here to illuminate things."

"I'm on my way," Sheppard agreed, motioning for Teyla and Lorne to follow him.


	3. It’s not like you’re being unfaithful

**Authors Note:**

Apologies to anyone who reviewed recently and is wondering where my reply is ... I haven't been getting any messages from fanfiction for over 24 hours now even though I know there should be some there so I haven't been able to respond. Thanks for your comments and I will respond when fanfiction lets me have your messages! And now, on with the next chapter.

**Chapter 3: It's not like you're being unfaithful**

"When you said illuminate things I didn't realise you meant literally," Sheppard looked into the pitch black structure with interest. He was standing in front of a small square building that had been almost overrun by trees in the thickest part of the forest. The whole place had an air of neglect and abandonment that convinced everyone noone had been there for a long time.

"Oh very clever," Rodney retorted. "Can you just step into the doorway and see what happens?"

"Didn't you already do that?" Sheppard looked back in time to see the uncomfortable look on Rodney's face and catch Ronon's obvious amusement.

"We all know there are times when only the natural gene will do," Rodney excused his inability to get the lights to turn on.

Chuckling at Rodney's continuing irritation that all things Ancient came so much easier to him, Sheppard turned back to the doorway and took a step inside. The lights flickered for a moment before coming on brightly.

"Figures," Rodney muttered, almost glaring at the lights that seemed to be mocking him with their luminiscence.

"Tell me again McKay - why did you pick this place up when all our others teams didn't?" Sheppard hesitated to proceed, feeling that frission of something inside that warned him to be on the lookout. He hadn't missed the significance of being 'invited' to a planet that just happened to have something Ancient on it.

"Because they're all incompetent," Rodney used the classic snarky tone that had made more than one member of his staff cry. "Look, the scans I run are much more complex than the standard stuff. The signal was very weak and this place is a long way from the village and the Stargate."

"So you're saying if those other teams had someone as brilliant as you along for the ride we'd have found this place before?" Sheppard said somewhat tongue in cheek, his gut feeling abated somewhat by Rodney's explanation.

"Something like that," Rodney said smugly, moving up to shoulder past John on his way into the facility.

"Hang on McKay," Sheppard held him back with ease. "We have no idea what to expect ... Ronon and I will check it out first."

"I hardly think a Wraith is going to be sitting in wait for us Colonel," Rodney said sarcastically.

"And yet it wouldn't be the first time we visited something deserted for millennia and found exactly that!" Sheppard reminded Rodney of their ordeal on the planet near where they'd discovered the Lagrange Point satellite. It had been more than two years but Rodney still cringed at the memory of what had happened to Doctor Gaul.

"Point taken," Rodney stepped back immediately. "After you." He gestured expansively.

"Thank you Rodney," Sheppard exchanged a wry grin with Ronon before glancing across at Lorne. "Major, you'll stand guard at the door ... make sure no one follows us in."

"Yes Sir," Lorne took up a defensive position back from the doorway, weapon at the ready.

Sheppard and Ronon stepped fully into the structure. The corridor they were in opened up into a single room – with no markings or decorations of any kind it was impossible to even speculate on what it had been used for, although the flavour was decidedly Ancient. With no threats evident Sheppard radioed for Rodney and Teyla to join them.

"This place is empty!" Rodney gazed around in disbelief. "I don't believe it."

"Energy signal," Sheppard reminded him.

"Oh – right," Rodney consulted his scanner screen before walking slowly towards the furthest wall. "It's this way," he reported.

Sheppard moved to follow him ... when he got within one pace of the wall a panel just above head height lit up, flashing a beacon that seemed to shout 'over here!'

"McKay?" Sheppard looked to Rodney for some kind of explanation.

Rodney waved a hand over the panel but nothing new happened. Stepping back he motioned for John to do the same. Sheppard raised his hand ... before he'd even gotten half way through the swiping motion the panel slid open to reveal what looked a lot like a storage locker.

"The energy reading _is_ coming from there," Rodney confirmed.

Raising himself up onto the toes of his boots Sheppard could just barely see inside ... reaching up a hand he groped around before coming out with a small device that looked very similar to the Ancient life signs detectors. Of course it lit up as soon as John touched it, humming faintly as it threw out it's Ancient blue light. Stepping away from the wall Sheppard held out the device for Rodney to see. "Is this what I think it is?" he asked in surprise.

"Ah ...," Rodney paused, taking the data pad and pressing the usual buttons. "No ... unless it's malfunctioning almost beyond recognition. I think it's something to do with communications ... I can't be sure though without getting a translation for some of this text."

"Okay, so mission accomplished?" Sheppard waited until Rodney realised some kind of response was expected.

"Yes, yes," Rodney turned back to the wall, distracted again. "No wonder we never picked this place up before ... it looks like the Ancients took everything else with them that might have alerted us."

"That thing was dormant until I touched it McKay," Sheppard reminded him that it couldn't have been the source of the energy reading they'd picked up.

"I know," Rodney agreed. "It's pretty cool actually. The storage locker itself is the source ... it's got some kind of reminder system with a lowgrade energy signal attached ... just enough to alert someone it was there after a certain period of inactivity. Maybe the device has something more to explain why." Rodney bent his head over the datapad, completely oblivious to his surroundings.

Sighing impatiently Sheppard snatched the new data pad from Rodney's hands, jamming it into a pocket on his vest despite Rodney's protests. "You can play with your new toy later McKay," he drawled. "It's time to go home."

They walked back to the Stargate with little conversation, Sheppard keeping an eye out for potential threats while his thoughts reviewed the events of the day. On the surface everything seemed reasonable, including Rodney's explanation for why they'd never found the Ancient structure before. Still, coincidences like what he'd experienced that day never sat well with Sheppard. McKay would have to do a good job convincing him everything was above board before he'd authorise any kind of further action resulting from this mission.

oOo

A week later Rodney called Sheppard to his lab with the usual excitement in his voice, greeting him impatiently when he walked through the door a few minutes later.

"You're gonna want to see this," he said with that smug expression he often got. "I've been translating the text on that communications data pad we found and I think I've worked out what it was for."

"Well don't keep me in suspense Rodney," Sheppard drawled.

"It's an add-on for the Control Chair," Rodney said it like John would understand immediately what that meant.

"For what purpose?" Sheppard asked in exasperation. "I assume we're not talking a rumble pack here!"

"You and your juvenile pass times," Rodney countered. "No, no ... it's more like extra RAM. It expands the communications capabilities of whoever's operating the chair. I can't be 100 percent sure without testing it myself but I think it allows the user to talk to Atlantis just like you do!"

"What?" Sheppard looked at Rodney in open disbelief.

"You won't be the only one who can talk to the city anymore," Rodney reduced it down to the bit he knew John would be most interested it.

"Ah ...," Sheppard hesitated, not sure what to say in response. Realising there was only one step he could take next he turned his thoughts internally. "_Are you aware of any projects designed to help others talk to you like this?_"

"_There were discussions about developing a way to give the Command Chair that capability_," Atlantis revealed.

"How come you never mentioned it before?" Sheppard asked aloud.

"_There was some concern during early development that it might affect our awareness adversely_," Atlantis chorused that explanation. "_To avoid such an effect the project was moved to an off world location_."

"When was this?" Sheppard continued, after pausing to quickly fill Rodney in on the city's answers so far.

"_Many years before the Ancestors abandoned the city_," Atlantis replied. "_The war with the Wraith was in its infancy and the Lanteans were still engaged in research beyond defence against their enemy_."

"Is there anything in the database that would help explain it, additional to what Rodney's already accessed?" Sheppard smiled when Rodney perked up at that question.

The flashing list of file locations that appeared on Rodney's lab display was the city's answer to that.

"Check all of those files McKay," Sheppard ordered. "When you've exhausted that we'll need to report to Elizabeth and work out what we want to do with that device."

"I was thinking plug it in," Rodney said in a disappointed voice.

"I'm not saying we're not gonna do that McKay," Sheppard replied. "I just think we need to be very cautious – after all this is Atlantis we're potentially messing with."

"Of course," Rodney rallied his enthusiasm, turning back to the screen and beginning with the first file.

Sheppard watched him for a few moments before turning without a word and heading back to the Control Room. He spent the afternoon running security checks on the base, deliberately keeping his mind away from what Rodney had discovered. Soon enough it was evening and he found himself alone in his quarters with nothing to do but think.

"Would you want us to plus that thing in, if it turns out to be what Rodney thinks it is?" he turned to Atlantis for help.

"_Do you tire of being our only connection to your people?_" Atlantis countered.

"Of course not," Sheppard denied firmly. "But I'm just one person. Wouldn't it be ... safer if there were others who could communicate with you like this – for example in an emergency?"

"_There is some merit in what you say_," Atlantis agreed. "_Your ancestors felt the same, hence their pursuit of that particular project_."

"And yet you sound reluctant," Sheppard frowned at the concept, not sure the city was even capable of experiencing reluctance."

"_We have become accustomed to your mind John Sheppard_," the city's chorus was meek and to a degree even petulant. "_We are not sure we relish the thought of making such a deep connection with another._"

"It's not like you're being unfaithful," Sheppard joked. He sighed before attempting to explain his thoughts. "You knew after the Tria came back how much it troubled me to leave you to silence because I wasn't here. What if something happened to me and you were left like that forever?"

"_Nothing will happen to you_," the voice of Atlantis rang sharply in John's head. "_While you are in the city we exist to protect you. We trust that you are careful in your dealings off world._"

"I never plan to go out and be reckless," Sheppard said defensively, suddenly aware that all too often he _did_ come back to the city a little ... banged up. Returning back to the original topic John asked again. "Are you receptive to trying out this communications device? Remembering that it's not like we couldn't just pull it out again if you don't like it."

"_We will consider it, should the Control Chair add-on prove viable_," Atlantis agreed. "_As long as you remain aware that we wish for you to continue as our primary point of contact._"

"Agreed," Sheppard acknowledged the request with a self depreciating smile. While he'd never asked for such an intimate connection with the city he couldn't deny that he felt somewhat ... possessive of his unique bond. He knew the contradiction in that ... feeling that Atlantis was his alone while at the same time not wanting to be the only one who could talk to her. Knowing Atlantis felt the same possessiveness, despite his recent attempts to establish some distance, eased the tension he didn't know he'd been feeling since Rodney had told him what the device likely did.

This was gonna be interesting.

**Authors Note:**

Just wanted to add for those who don't know - a rumble pack is a plug in for a games controller that makes it vibrate etc during game play - for example when you play a racing game the controller will shake and 'rumble' when you're driving over rough terrain (or when using the wall to keep you on the track which I do too often lol). Makes the experience more realistic :D


	4. I already tried that too

**Chapter 4: I already tried that too**

"I was right," Rodney reported to the rest of Team Sheppard and Doctor Weir two days later. "The device we picked up on M4R 379 _is_ a communications add-on designed to give the user of the Control Chair additional access to the Atlantis awareness. There was nothing in the files Atlantis provided about completing the project but their plans match the schematics for the actual device exactly. There's no doubt they intended for the Control Chair to have this new capability."

"So anyone with the ATA gene could talk to the city as John does?" Elizabeth quizzed.

"Probably not," Rodney said reluctantly. "The Control Chair requires a fairly strong gene presence – Sheppard's the only one who's been able to do much more than just light up the systems."

"So where's the advantage then?" Sheppard asked impatiently.

"Because it might not require much more than lighting up the Chair," Rodney suggested. "Look, there'd be no point in the Ancients designing something that required the same depth of gene control as that required to talk to Atlantis without assistance. That just wouldn't make any sense!"

"And of course everything we've discovered about the Ancients makes perfect sense," Sheppard retorted, his anger over some of their recent actions fueling his sarcasm.

"There've been a ... few instances with obvious contradictions," Rodney admitted, "but I don't think this will be one of them."

"And what does Atlantis think about this?" Elizabeth asked curiously.

"She was receptive to the idea," Sheppard revealed, "but a bit wary as well. She requested that, regardless of the level of success with this thing, I still remain her primary point of contact."

"It would be uncomfortable to make such an intimate connection with a virtual stranger," Teyla nodded in understanding.

"I guess," Sheppard agreed uncomfortably. "In any case, if Rodney can reassure Atlantis that the device will do what it's intended to do, she's willing to participate in a trial."

"Okay then," Elizabeth made her decision. "Having backup for Colonel Sheppard would give us a potentially strong advantage should the city come under attack. It's worth the risk to investigate this device a little further. You have a go to plug it in Rodney."

"All right," Rodney jumped up excitedly, motioning for Sheppard to follow him. "Let's go down to the Control Chair and rig up some monitoring equipment."

"You want to do this right now?" Sheppard asked in surprise.

"No time like the present," Rodney replied with his 'I'm a man on a mission' demeanour firmly in place. Not waiting for any further response Rodney headed towards his lab, assuming Sheppard was following behind. Casting a somewhat plaintive look back at the others, John let himself be reluctantly drawn away.

oOo

"You're _sure_ this won't hurt Atlantis?" Sheppard asked hesitantly, hovering near the Control Chair as he watched Rodney work.

"As sure as I can be,' Rodney said confidently. "The schematics all check out and really there's no way to test this thing other than plugging it in."

"And there's nowhere else we can do that," Sheppard acknowledged.

"Only one Atlantis," Rodney quipped with an easy smile. "Are you ready?"

"Carson, you ready to try this?" Sheppard turned to the nervous Doctor expectantly.

"No I'm bloody well not," Carson retorted. "You know how I feel about that chair!"

"Lighten up Carson!" Rodney exclaimed. "It's not as if you can hurt anything – Sheppard turned off drone launch capability along with anything else you could possibly use to do some damage. The Chair is perfectly safe."

"Easy for you to say Rodney," Carson muttered. "You didn't almost blow up a General and one of your eventual best friends the first time you sat in it."

"It's been three years Doc," Sheppard put a hand on Carson's shoulder and squeezed reassuringly. "I think you're ready for a whole new future with the Control Chair."

"If you say so Colonel," Carson agreed less than convincingly. "Let's get this over with then shall we?"

"Right," Rodney turned to John expectantly. "You want to check with Atlantis one last time?"

"Atlantis is fully on board with this," Sheppard said aloud. "_That is right, isn't it?_"

"_We are content to participate in this trial_," Atlantis agreed. "_Doctor Beckett is a dedicated member of your team_."

"We're good to go," Sheppard gave Rodney the green light to proceed.

"Wait - how will I know this is working?" Carson asked suddenly, halting Rodney just as he was about to plug the add-on into the chair.

"Trust me - you'll know," Sheppard replied confidently. "You heard me talk about what happened with me ... you know what to expect."

"But what do I say to her?" Carson persisted nervously.

"This isn't a date Carson!" Rodney retorted. "Just speak with Atlantis if the connection is there, ask her the question Sheppard set up. If you give us the right answer we'll know it worked."

"It'll be fine," Sheppard reassured him. "Atlantis likes you Doc – she's looking forward to meeting you personally."

"Oh," Carson smiled enough for his dimples to appear, obviously flattered by that. Moving over to the Chair he sat down slowly and closed his eyes, the Chair lighting up after a few moments of obvious conscious effort on his part.

Rodney inserted the data pad into the slot that seemed to have been designed for just such a purpose, pausing a moment before resolutely pushing it all the way in. There was an audible click as the two pieces of technology connected, but there was no visible change in the Chair or its occupant. They would have to wait until Carson was finished to find out whether the trial was a success or not.

"You know it's lucky we have a ZedPM," Rodney muttered in an aside to Sheppard. "This wouldn't have been possible without it. Of course having three ZedPM's would have been better."

"Is it working?" Sheppard drew Rodney's attention back to the task at hand.

"The add-on has interfaced successfully," Rodney consulted his readouts before reporting. "Carson should be asking his question right about now."

Carson sat up abruptly, an expression of awe on his face. "That was ... Atlantis is an amazing lady," he looked over at Sheppard with a new respect. "I never realised how hard that level of communication is on the brain ... I'm surprised you can put up with that on a continual basis."

"You get used to it," Sheppard dismissed the implied compliment lightly. "Did you talk to Atlantis?"

"Aye," Carson agreed with a bemused smile.

"And the answer to my question?" Sheppard raised a brow quizzically.

"Atlantis kissed you when you met her in Aperio's computer reality," Carson obediently replied.

"Get your mind out of the gutter McKay," Sheppard drawled, amused by Rodney's horrified and sickened expression. "It was a kiss on the cheek - she looked like my Grandmother!"

"Not the question I was expecting," Rodney admitted.

"It was the only thing I could think of that fit the criteria – something I never told anyone that the real Atlantis would know," Sheppard explained.

"So it worked," Rodney's face glowed with the triumph of scientific success. "It actually worked!"

"Looks like it," Sheppard agreed, giving Rodney a few moments to wallow in his victory. "Time to pull the device McKay – I promised Atlantis this would be a short trial only."

"Of course," Rodney jumped up and went back behind the Chair. There was silence and then a few muffled curses. More silence and a more heated curse. "_Oh come on!_" Rodney muttered, the sounds of fingers tapping way too hard on a computer tablet carrying easily across to John's position.

"Problems McKay?" Sheppard quizzed, walking around the chair to gaze down at his friend.

"Maybe?" Rodney looked up in concern. "I've input the command to expel the add-on but ... it's not working."

"Try again," Sheppard replied insistently.

"_I have_," Rodney admitted. "I tried a number of different commands – one of them should have worked!"

"Then we'll have to just rip it out," Sheppard decided, shifting Rodney aside so that he could grab the two or three inches of data pad sticking out of the slot. His face contorted as he strained to pull the device from the chair ... without success.

"Give it up muscles," Rodney said sarcastically. "I already tried that too."

"So this thing it stuck?" Sheppard said grimly.

"It's stuck," Rodney agreed, looking both apologetic and just as grim.

**Authors Note:**

Still not getting any messages from the fanfic website so once again apologies for not responding to your reviews ... it's not my fault honest, and I have no idea how to fix it. I just hope everything will just magically appear the next time I open my inbox ... hasn't happened yet and it's been two days. Anyways, hope you enjoyed this latest chapter.


	5. And the Chair functions normally?

**Chapter 5: And the Chair functions normally? **

"Why would that happen McKay?" Sheppard rounded on Rodney in agitation.

"I don't know!" Rodney complained. "Maybe it wasn't intended to be removed ... although there was nothing in the schematics to suggest that was part of the design. It's not necessarily a problem, is it?"

"I don't know _Rodney_," Sheppard almost growled. "I promised Atlantis this was a short trial and now you're telling me that device could be in there permanently. That sounds like a problem to me!"

"Can you render the device inert Rodney?" Carson was standing with Sheppard now too, expression firmly fixed into Doctor mode as though Atlantis were his patient.

"Okay, okay," Rodney's face took on the 'I have an idea' expression Sheppard looked for at times like this. "I'll try a complete shutdown of the Chair systems ... hopefully that will reset everything and allow us to eject the add-on."

"Do it," Sheppard ordered. He'd avoided making contact with Atlantis so far and she'd been strangely silent too. "_You okay?_" he thought hesitantly.

"_Conversing with Doctor Beckett was strange but not unpleasant_," the chorus responded. "_Without an operator in the Control Chair our awareness feels unchanged._"

"_So you can't feel the device unless someone's actually sitting in the Chair?_" Sheppard checked his understanding. "_You can't suddenly hear Carson or Rodney or anyone else with the gene?_"

"_We only hear you_," Atlantis replied, "_although we are aware the add-on is there_."

"_I'm sure McKay will fix this_," Sheppard thought bracingly. "_It just might ... take a while_."

"_We are well John Sheppard_," Atlantis reassured him. "_We would prefer the device be removed as soon as possible but we have not been harmed._"

"_That's a relief_," Sheppard replied. Turning back to Rodney and Carson he passed on that reassurance. "Atlantis is okay with this ... for now."

"Oh," Rodney's face relaxed just a little. "Okay ... you two might as well clear out – this is likely to take a while."

oOo

"Sheppard, can you come down to the Control Chair?" Rodney's voice in his ear interrupted Sheppard's conversation with Ronon and Teyla.

"We're having dinner Rodney," Sheppard complained. "Can't it wait?"

"_No_," Rodney retorted. "Some of us actually skipped dinner ... _and_ lunch so we could keep working. I need you to t- ... _do_ something before I can get any further."

Sheppard raised an eyebrow at Rodney's near slip ... he was obviously frustrated because usually he had better control of himself over an open radio channel with regard to John's secret. That raised an unpleasant thought ... the current problems with the Chair had been kept between his little group of 'in the know' people ... if more drastic action was required they might have to bring others into the loop. Before he knew it his little secret wasn't going to be a secret anymore ... and it was only a small hop from that to everyone at the SGC ... and IOA finding out. Pushing that unpleasant thought to the background Sheppard returned his attention to Rodney.

"Okay - fine," Sheppard stood up abruptly. "I'll be there in a few minutes."

"Is everything okay?" Teyla asked in concern.

"Yeah - Rodney just needs me to talk to Atlantis," Sheppard replied in a low tone. "I'll catch you guys later."

"Don't let McKay boss you around," Ronon called out as Sheppard turned to leave. Throwing a withering look back at his friend John strode from the commissary, making the short walk down to the Chair Room.

"Finally," Rodney muttered with an impatient look when John arrived.

"What do you need?" Sheppard looked at Rodney expectantly.

"The shutdown didn't work," Rodney admitted. "I need to know more about how that add-on is interfacing with the chair internally."

"And you want me to ask Atlantis," Sheppard finished with a considering look. "_You up to talking with McKay directly?_" he thought to the city.

"_We have heard Doctor McKay before_," the chorus was relaxed and untroubled. "_We will show him the device in a way he could not see otherwise_."

"_Thanks_," Sheppard replied, grinning at Rodney's impatient look.

"Well?" he demanded. "Can we get on with this? Ask her to describe the connectors between the chair and the add-on."

"Why don't you ask her yourself?" Sheppard said simply.

"What, you mean talk to Atlantis directly?" Rodney asked in disbelief. "I thought you said she only wanted to talk to you."

"I said she _preferred_ talking to me," Sheppard countered. "She can show you how the device is working from the inside ... something she can't do if we play pass on the questions and answers." Rodney's mouth literally hung open after John finished his explanation. Smiling ruefully for a moment Sheppard then put on his command face as he gave Rodney an order. "Sit in the chair McKay ... _now_!"

"Oh," Rodney dropped into the chair abruptly. "Right ... right."

Reclining the chair back Rodney closed his eyes and had his first real conversation with Atlantis.

"_Um ... hi_," his thoughts babbled much as he did verbally when he was nervous. "_I'm ah ... really sorry about all this ... and I just wanted to say thanks for, you know, agreeing to talk to me_."

"_John Sheppard thinks very highly of you_," the chorus sounded in his head, pulsing and vibrating in a way that made him feel very uncomfortable and on edge.

"_He does?_" Rodney was surprised. "_That's not ... that's ... nice. Would be nicer if he actually said something once in a -_."

"_Ask your questions and we will show you the answers_," the chorus cut him off, stopping his thoughts in an instant. Rodney was sure that even if he'd wanted to continue down that line he would not be able to. The power the city held over his mind was amazing and scary and frankly pretty disturbing. How did Sheppard put up with this all the time?

"_John's mental processes are much different from your own_," Atlantis let it be known that she was aware of _all_ his thoughts while he was sitting in the Chair - not just the deliberate ones.

"_Right_," Rodney frowned at that before mentally shaking himself. "_Right - can you show me how the add-on is connected internally_?"

A clear mental image appeared in his head ... Rodney studied it, asking more questions to clarify what he was seeing before he thought he had enough to make his conclusions. "_Can I get a picture of what you showed me - something I can show the others?_"

"_Of course Doctor McKay_," Atlantis chorused pleasantly. "_A new file has been flagged for your attention. Do you have any further questions?_"

"_Is making the add-on permanent consistent with what you know of the Ancients of that time?_" Rodney thought curiously.

"_We believe so_," Atlantis replied after a short pause. "_There was an ... incident in the city that troubled them greatly. The project to create the add-on was part of their response. They would not have wanted to leave any room for something similar to occur again._"

"_What incident?_" Rodney demanded.

Abruptly the Control Chair deactivated and he was thrust back into the upright position. Rodney rubbed a hand over his aching head with a confused frown. "I guess she didn't want to answer _that_ question," he muttered under his breath.

"What question?" Sheppard looked at Rodney curiously.

"Ah ... nothing," Rodney dismissed lightly. "I don't know how you do that all the time ... my head feels like its about to explode after only a few minutes."

"Practice ... and talent," Sheppard said smugly.

"More likely the Chair causes additional discomfort because we're forcing a connection unnaturally," Rodney discounted John's claim to superiority.

"Did you get what you need?" Sheppard brought the conversation back to the problem at hand.

"Yeah," Rodney revealed.

"So you know how to remove the add-on?" Sheppard persisted despite Rodney unusual lack of explanation.

"Not exactly," Rodney prevaricated. "I need to follow up on a couple of things ... just give me half an hour and then I'll fill you in along with the others."

oOo

"As you all know," Rodney reported to everyone a short time later, "I tried a systems shutdown auto eject as well as attempting to remove the device physically while the Chair was completely dead. It didn't work."

"So the add-on device _can't_ be removed?" Elizabeth looked at Rodney with concern.

"Not by any method I know of," Rodney admitted. "And that's not the worst of it."

"There's more?" Sheppard's voice was tinged with anger ... he'd let himself be convinced the device wasn't dangerous and after Rodney's talk with Atlantis he'd been hoping for a better outcome.

"Unfortunately yes," Rodney spoke resolutely, determined to report everything despite his continuing feelings of guilt over the whole thing. "Atlantis showed me what was going on internally at the point where the data pad is connected. She gave us this." Rodney called up a picture on the main display screen.

"What are we looking at Rodney?" Doctor Weir asked curiously.

"A kind of x-ray of the Chair," Rodney offered. "The interesting part is right here," he pointed to a spot a few inches away from the main connection. "These are _physical_ cable connections. And they're not all - there are component bridges and even some power crystal overlaps evident too. If I'm reading this right the data pad is stuck by design."

"I thought you said there was no evidence of that in the schematics," Sheppard said accusingly.

"There wasn't," Rodney reaffirmed defensively. "Look, for some reason the Ancients decided to alter the design _after_ they removed the project from Atlantis. They never meant for the add-on to be removed. I asked Atlantis if that was consistent with their behaviour at the time and she said it was. Something happened ... some kind of incident that I think needed them to be able to talk to Atlantis. For some reason they couldn't - they meant that add-on to be the solution if it ever happened again."

"Did Atlantis explain this incident to you?" Teyla asked curiously.

"No," Rodney admitted. "In fact she chucked me out of the system when I asked. I checked all the records around the timeline she gave us ... there was nothing."

"If it represented some kind of weakness then they might have deleted it to protect the city," Sheppard offered. "I could press her ... see if she'll tell me more."

"Let's hold off on that for the moment," Elizabeth decided. "Was there anything back at the outpost that would explain all this better?"

"We didn't find anything the first time but we weren't exactly looking," Sheppard replied. "We could go back to the planet now - see what we can find?"

"Prepare your team and head out as soon as you're ready," Elizabeth agreed.

oOo

"This isn't my fault," Rodney's tone pleaded with John for something ... forgiveness maybe?

"I know McKay," Sheppard let him off easily. "Despite your little foray in the Control Chair you have no idea how this is affecting Atlantis. Nothing she'd admit to but I can tell she really wants that data pad removed from her systems. I just need to offer her something ... even if it's just a proper explanation on why they made that device a permanent fixture. If we're lucky they had a way to remove it too."

"Let's hope so," Rodney agreed, falling into step beside the Colonel as they headed for the Gateroom.

"We'll head straight for the structure," Sheppard spoke to his team before the Gate was dialled. Looking up at the Control Room he requested the dial up. "Let's move out."

oOo

"This place is as devoid of information as it was last time," Rodney complained, having exhausted every idea he had for finding out more. He'd even insisted that Sheppard swipe his hands over all the wall panels, hoping that one of them would be another storage locker like the one they'd found the device in. Sadly that hadn't proved the case.

"Perhaps Tomaskitous knows something," Teyla offered that suggestion without much hope.

"Who?" Rodney frowned in confusion, slumping down tiredly against the nearest wall.

"Tom - the village leader," Sheppard explained. "It's unlikely ... he said last time he was unaware of any Ancient structures here. Besides – I'm not that keen on going back there."

"Being the village legend not all it's cracked up to be?" Rodney quipped.

"Not exactly," Sheppard drawled sardonically. "Have you got any other ideas?"

"None," Rodney hauled himself back to standing. "Face it – there's nothing here."

"Agreed – let's get out of here," Sheppard motioned for the team to form up and head back to the Gate.

oOo

"Do we know what the long terms effects of leaving the data pad plugged in are likely to be?" Doctor Weir asked after Team Sheppard had reported its lack of success.

"There's no way to know for sure," Rodney pointed out, "but on the surface it seems like there's no effect at all. I've been running a continual monitoring process on the Chair and I haven't picked up anything so far."

"Colonel, has Atlantis given you any indicator that the add-on _needs_ to be removed?" Elizabeth looked at John expectantly.

"No," Sheppard admitted reluctantly. "She says it's not doing anything to her ... she just doesn't like the idea that anyone can sit in the Chair and talk to her."

"So the Chair functions normally?" Elizabeth continued.

"Every test we've run says yes," Rodney confirmed.

"All right then. For now I see no choice but to assume the add-on is doing what was intended by the Ancients," Elizabeth concluded. "Keep trying to come up with a way to remove it Rodney, and continue to monitor the Chair systems closely just in case. Should the need arise we now appear to have a permanent way for any ATA gene holder to communicate directly with Atlantis ... we'll respect the city's wishes however and keep to the communication channels we've already established." Elizabeth smiled at Rodney's crestfallen expression. "That's right Rodney – no long conversations about your latest projects."

"I was just gonna ...," Rodney trailed off miserably at Elizabeth's stern look. "Fine, no communication direct with Atlantis unless it's an emergency and Sheppard isn't available."

"_I'm sorry_," Sheppard thought softly. When there was no reply he pushed a little harder. "_Hello?_"

"_It was not your fault_," the chorus responded. "_We agreed to the trial knowing the risks and Doctor McKay is right ... none of our systems have been affected. In time we will become used to the presence of these additional capabilities._"

"_Okay,_" Sheppard agreed. "_Just ... let me know immediately if you sense any kind of problem because of that data pad._"

"_We thank you for your concern_," Atlantis acknowledged his request.

**Authors Note:**

Sorry for the late post today ... I wasn't happy with this chapter so I rewrote a fair bit of it ... still not happy but I'm releasing it to you anyway. Also I'm back on the air with fanfic messages so I can reply to reviews as per usual. Thanks for your patience!


	6. I’ll get Rodney to check it out

**Chapter 6: I'll get Rodney to check it out**

"_John Sheppard?_" Sheppard woke abruptly in the depths of the night to the sound of Atlantis speaking in his head.

"What?" he sat up, rubbing a hand over his face as he brought the lights up half way. "Is something wrong?"

"_We are detecting a sudden increase in the temperature within the lowest levels of the city_," Atlantis reported urgently.

"What, like before with the hydrothermal vent?" Sheppard was fully awake now, already pulling on his uniform in preparation to act.

"_Yes, the readings are very similar_," the chorus agreed.

"Okay, leave it with me," Sheppard said confidently. "I'll get Rodney to check it out."

"_Thank you_," the harmony of voices was more relaxed now that something was being done.

Sheppard walked down the darkened corridors, arriving at Rodney's door a couple of minutes later. He swiped a hand over the door controls, waited for some response and then activated them again. He could hear the chiming from outside – how the hell could Rodney sleep through that? Using his command override Sheppard opened the door and took a couple of steps inside.

"McKay," he whispered urgently, but got nothing. "Rodney – wake up!" he said in a normal voice.

"No," Rodney mumbled, head buried in his pillow. "Still got plenty of time to ..."

"McKay!" Sheppard strode over to the bed and shook Rodney urgently.

"What?" Rodney turned over and squinted up at John. "Why are you in my room at ...," he glanced over at his clock, "3 am?"

"Atlantis is picking up an environmental problem in the lower levels," Sheppard said insistently. "I need you to run some diagnostics."

"And it couldn't wait like three hours?" Rodney asked incredulously.

"No," Sheppard denied. "She said it was similar to what happened with the hydrothermal vent. It sounded urgent."

"All right," Rodney sighed before rolling himself out of bed. "Meet me in the Control Room."

Sheppard nodded, turning and leaving Rodney to get up.

oOo

"I'm still not reading anything," Rodney complained two hours later. Sheppard had dismissed the night shift early, so it was just the too of them in the darkened and deserted room. "You know it's unlikely we'd have another situation like that happen again don't you?"

"I'm sure volcanic activity on the ocean floor isn't the only way the city could heat up," Sheppard retorted.

"Look, I don't know what to tell you," Rodney rubbed a hand tiredly over his eyes. "I've run this diagnostic twice already with the same result. The control systems would have sounded an alarm if the environmental readings were outside the normal range – with the ZedPM we can run all the sensor systems continuously, including the midrange ones. They would detect any kind of problem outside the city."

"So Atlantis was wrong?" Sheppard looked at Rodney incredulously. "Is that even possible? I mean, isn't she like a summary of all the systems, including the ones you just mentioned?"

"I would have said no before this morning," Rodney agreed. "Let me run some other more detailed diagnostics. In the mean time you should speak with Atlantis ... try and find out more about what she was detecting."

"Okay," Sheppard settled back in his seat, watching for the first staff to turn up for the morning shift while at the same time carrying on his conversation. "_Rodney hasn't found anything_," he thought at the city. "_Are you still picking up those increased temperatures?_" There was no immediate response and Sheppard frowned in concern. "_Atlantis?"_

"_We apologise John Sheppard_," the chorus intoned. "_It appears there was an error in the midrange sensor system that caused us to access historical readings_."

"_From when the hydrothermal vent really was threatening the city?_" Sheppard asked.

"_That is correct_," Atlantis agreed. "_When Doctor McKay ran the first midrange sensor diagnostic he corrected the error. We are now reading current information about the environmental conditions_."

"_What caused the error?_" Sheppard persisted. "_Is it something that could occur again?_"

"_We do not believe so_," Atlantis reported. "_It is not uncommon for large files to be separated within our system. The usual regular maintenance procedures serve to rejoin connections and ensure all systems run efficiently_."

"_Oh ... okay_," Sheppard slumped down in relief. "You can stop checking Rodney," he said aloud. "Turns out there never was a temperature increase. Atlantis said one of the midrange sensor files got split inside the system – she was accessing historical data without the reference to tell her that."

"Ah," Rodney nodded in understanding. "I'm guessing when I ran the diagnostics the problem corrected itself. Still ... such an obvious file separation is an issue. I'll just check the defrag subroutines in the maintenance system and make sure they're working properly."

"Atlantis has _defrag_ subroutines?" Sheppard asked in amazement.

"Not exactly," Rodney admitted, "but they're close enough to what happens on our computers and it saves on confusion to call them that. Atlantis isn't that different from us in that respect actually. Files get fragmented within the systems during processing and end up spread throughout the storage medium. Over time the spread gets wider and wider ... that's when the systems slow down or processing errors occur. It's standard practice to run defragmentation routines to join the files back together again."

"If it's standard practice then why are you checking the subroutines?" Sheppard asked curiously.

"Because this is the first time in nearly three years that I've noticed a detectable problem caused by fragmentation," Rodney replied simply. "It's probably nothing but ... better safe than sorry."

"Do what you have to," Sheppard agreed, getting up and leaving Rodney to it.

oOo

"What's the status on that fragmentation problem?" Sheppard checked back with Rodney a couple of days later.

"It's actually a lot more interesting than I was expecting," Rodney replied. "It appears that files are being fragmented more distantly within the storage medium than usual."

"Is that an issue?" Sheppard frowned worriedly.

"It's a maintenance issue," Rodney replied casually. "I'm still looking into why the system would be separating files like that but the defrag routines are handling it with ease. There are some historical records that suggest this has happened in the past so I don't think it's a major problem."

"Well keep an eye on it anyway," Sheppard replied sternly. "We don't need another apparent emergency that turns out to be a walk down memory lane."

"Right," Rodney agreed. "I'll set up something to keep track of it. Why don't you check with Atlantis ... see if she's aware of anything out of the ordinary."

"_Are you picking up this file fragmentation thing?_" Sheppard immediately turned his thoughts to Atlantis.

"_All our systems are operating as normal_," the chorus reported in easy tones. "_The minor issue with the midrange sensor files has not been repeated elsewhere_."

"_That's good. Can we -_," Sheppard was interrupted from asking Atlantis about anything else they could do by a general annoucement over the city wide intercom.

"Colonel Sheppard and Doctor McKay, please report to the Containment Lab."

Sheppard looked across at Rodney curiously. "Are you running anything in there?"

"Not since the whole zero point vacuum energy fiasco," Rodney replied, getting up and following Sheppard from the room. "In fact nothing should be going on in that Lab ... we closed it off after we depleted the last ZedPM."

"Well something's obviously going on now," Sheppard turned a corner and headed down the right corridor. A marine was waiting at the door, obviously assigned by Doctor Weir to keep people out. Exchanging a worried look with Rodney Sheppard motioned for the guard to let them through.

Inside the boards were all lit up and the pulse of the generator could be heard clearly. A group of marines formed a line, standing at attention across the room ... Zelenka and one of his staff were squinting at a display on a console in the middle of the room. Doctor Weir moved towards them as soon as they appeared in the doorway.

"Elizabeth?" Sheppard look to her for an explanation.

"Doctor Zelenka noticed an anomalous energy spike a short while ago and traced it down here," Elizabeth replied. "It looks like we're on the other side of an attempt to bridge between parallel universes."

"This is bad," Rodney muttered sickly. "Do you know how much power it took to shut one of these down last time?"

"Almost a ZPM's worth," Elizabeth replied, her look reminding Rodney of how it was they'd all come by that knowledge ... especially his part in it. "However, we have an even bigger problem."

"Bigger than potentially ripping a hole in the fabric of multiple universes?" Rodney asked in amazement.

"Yes Rodney," Elizabeth said simply. "Just before we called you down here there was a surge of power within the chamber. They sent someone through."

"Please tell me it's not another McKay," Sheppard begged. "We were lucky to get rid of the last one."

"Oh har har," Rodney's tone was insulted, even though he hadn't actually liked the alternate Rod himself.

"Have a look for yourself," Elizabeth invited, motioning for the Marines to step aside so they could look inside the containment chamber.

"Sheppard!" General Jack O'Neill called out a greeting. He was dressed casually in green BDUs, grey hair just a bit scruffy, looking much the same as he had the last time Sheppard had seen him. Currently he was sitting mostly inside the chamber, feet hanging over the side, upper body crouched uncomfortably in the tight space. "It's about time! Get me out of here."

"The General asked specifically for you John," Elizabeth revealed weakly. "He says he's from the future."

**Authors Note:**

Thank you to **hermit hideaway** who gave me the idea all the way back at the first story for General O'Neill to visit ... this probably wasn't what you had in mind but ... I just hope I can do him justice!


	7. I’m glad you approve

**Chapter 7: I'm glad you approve**

Sheppard kept his eyes on the General as the two Marines he'd motioned over assisted O'Neill out of the chamber. He'd be escorted to a nearby Isolation Room where he'd stay until such time as Sheppard was ready to talk to him. And okay, sure, he _was_ a General but he wasn't _their_ General ... and it wasn't like Sheppard was putting him in the brig or anything.

"The future?" John turned to look at Rodney with a raised brow.

"Theoretically it might be possible," Rodney revealed. "The bridging concept applies to parallel universes in both space and time."

"Isn't having that bridge connected going to cause the same problems here as our experiment did in Rod's universe?" Elizabeth asked worriedly.

"Maybe, maybe not," Rodney said thoughtfully. "It's possible they found a way to stop exotic particles from building up but I need to do a lot more analysis before I can say for sure."

"What possible reason could there be for him to come here?" Sheppard frowned in confusion.

"No idea," Rodney said unhelpfully. "In fact there's no guarantee he even meant to travel to this specific universe and time. We were never able to control the connection of the universe bridge to that extent although we did work out it was possible to send matter through the bridge from either side."

"Well maybe they got better at that in the future too," John retorted. "We need some answers McKay."

"My guess is they want some kind of help they can't get in their own universe," Elizabeth suggested. "Since General O'Neill asked for you John, it's likely something only you can do. The only way we'll know for sure is to speak with him."

"We'll let Carson check him out first," Sheppard's tone was just shy of commanding ... given that an intruder in Atlantis fell very clearly on the side of a military situation he was firmly in charge. "Rodney, start analysing that connection – see if you can confirm the General's story - and find out if we're in danger!"

Not waiting for a response Sheppard turned and headed straight for the infirmary to talk to Carson, Elizabeth following at his side.

oOo

A couple of hours later, up on the Observation Deck, they watched as O'Neill paced around impatiently. He seemed oblivious to his surroundings until he looked up and saw Sheppard and Elizabeth watching him.

"_Oh for cryin' out loud_!" he shouted impatiently. "Your Doctor Beckett would have run enough tests by now to confirm that I'm who I say I am. We're wasting time – I need to explain why I'm here."

Carson _had_ reported to them only moments before that based on every test he could think of to conduct the man down in that room _was_ General O'Neill. Sheppard glanced at Elizabeth questioningly. She nodded, giving her agreement that the next step had to be talking to the General personally.

"Rodney," Sheppard tapped his earpiece to make contact. "Have you got anything yet?"

"Still working," Rodney said briskly.

"Put it on hold for now," Sheppard ordered. "We're gonna talk to O'Neill ... meet me outside the Isolation Room."

oOo

"You say you're from the future," Sheppard began, sitting across from the General with Rodney at his side. "Got any proof?"

"_No_," O'Neill said somewhat irritably. "Anything I could tell you about the future would be pointless – you'd have to wait to find out I was right and we don't have that kind of time."

"But if you're from an alternate future wouldn't you have taken the pressure off as far as time goes?" Rodney frowned in confusion. "Unless ... you picked this specific universe deliberately?"

"I said I was from another time," O'Neill replied, "I never said I was from another universe."

"You're ... our General O'Neill?" Sheppard glanced at Rodney and got a shrug in reply to the unspoken question of whether that was possible too.

"Wouldn't be much point in travelling to the past otherwise, now would there?" O'Neill smiled at Rodney's obvious scepticism. "Your future self knew you'd react like this. He gave me the laptop Sheppard's security guys appropriated – everything you need to convince you is on that."

"We'll save the scientific explanations for later then," Sheppard drew O'Neill's attention back to him. "Let's just assume for the moment that you _are_ from our specific future ... why come here? Why now?"

"Finally the right question!" O'Neill smiled at Sheppard approvingly. "We had a problem with the city in my time ... a pretty big problem actually ... caused by something you're _going_ to do. I'm here to stop you from doing it."

"What do we do?" Rodney's voice was slightly panicked now. "How bad is it?"

"You been on that mission to M4R 379 yet?" O'Neill asked John. "The one where Major Lorne was held hostage for half a day until you showed up?"

"Yeah, about three weeks ago," Sheppard revealed.

"And I'm guessing you found a very interesting Ancient data pad on your way back to the gate," O'Neill waited until both men nodded. "McKay's checked it out and it looks good ... so you're probably thinking about using it. Don't. Destroy it or not, your choice ... but whatever you do, don't plug it into the Control Chair."

"_That's gonna be just a tad difficult because we already did_," Sheppard almost growled, scowling at O'Neill in exasperation. Rodney's face had that 'I've just discovered a disaster' look but he was unusually slow to translate it into speech.

"Crap!" O'Neill's laid back attitude disappeared in the blink of an eye. "Why the hell did you do that?"

"You're from the future," Sheppard reminded him grimly. "You already know the answer."

"How long?" O'Neill was all business now.

"A couple of weeks," Rodney revealed weakly. "We tried to remove it but ... ah ... we couldn't."

"And you've already worked out that it was designed that way," O'Neill didn't wait for Rodney to acknowledge that. "Your future self did give us an alternative plan but it's gonna be a lot more difficult this way."

"Then why didn't you get here _before_ we plugged that damn thing in?" Sheppard drawled angrily. "That would have been so much more helpful!"

"_I tried_," O'Neill defended insistently. "The vacuum chamber method of time travel ain't exactly a precise science!"

"You couldn't use a solar flare like everyone else?" Sheppard refused to be swayed from his annoyance, even though deep down he knew arguing over time travel methodology was ridiculous.

"Things have happened where I come from," O'Neill said cryptically. "Just trust me when I say there was a reason we couldn't use that approach and leave it at that. McKay had to develop a whole new science to pinpoint a specific spot in space and time. It took longer than we expected ... we couldn't afford the additional time to fine tune the targeting aspects."

"So I'm still a genius in the future?" Rodney smiled smugly.

"You of all people know I can't reveal more than the barest details necessary for you to act," O'Neill admonished.

"Grandfather paradox and all that," Rodney muttered in an aside to Sheppard. "I assume you've got a way to get back to your own time?"

"It's all on that laptop," O'Neill explained, looking sternly at Sheppard as he continued. "I suggest you let McKay look at it so we can get on with solving the problem."

"I'm still not sure we should believe you," John denied. "This is a pretty wild story you're spinning."

"Look at the laptop!" O'Neill's tone was frustrated at the need to repeat himself. "You know ... technically I outrank you Colonel," he drawled. "I could make that an order."

"Rodney," Sheppard kept his eyes on the General as he spoke, "check out that laptop ... let me know when you have something."

Rodney rose from his chair in uncharacteristic silence and hurried from the room.

"You gonna keep me locked up in here?" O'Neill leaned back in his seat casually.

"You're not our first visitor from across the universe bridge," Sheppard replied just as casually. "I'll assign you some quarters, give you free run of most of the base but you don't go anywhere without a military escort."

"Exactly what I would have done in your position," O'Neill said without offence.

"I'm glad you approve," Sheppard smiled sardonically.

oOo

"Found anything McKay?" Sheppard strolled into Rodney's lab early the next morning. "Is the universe bridge gonna blow us up? His attitude was cavalier because he'd already assumed if the news was bad he'd have heard about it sometime during the night.

"Plenty and no," Rodney turned to John with eyes bloodshot from lack of sleep.

"Have you been up all night?" Sheppard looked at him in concern.

"Yes," Rodney replied abruptly. "Zelenka and I went over all the readings from the Containment Chamber in combination with what's on O'Neill's laptop ... they managed to stabilise _and_ control the build up of exotic particles as well as the level of energy production because its primary purpose _isn't_ to create power. It's producing just enough to keep the connection alive and exotic particles are holding well within acceptable levels."

"Well that's a relief," Sheppard _was_ grateful to have one less thing to worry about.

"This stuff is amazing," Rodney said in wonder, "and I say that knowing it's the future me who developed it."

"Does the General's story check out?" Sheppard waited, knowing Rodney would feel compelled to give him a run down on the whole thing before answering the simple question.

"O'Neill wasn't joking when he said the future McKay created a whole new science to turn the zero point energy project into a time travel device. He expanded on Jeanie's bridge between universes concept ... the maths is ... well let's just say that it's at the limit of my current understanding. End result - theoretically it _is_ possible to target the home universe by bridging through a nearby parallel universe and back out again in a kind of loop. The loop is controlled so that its exit into the home universe is at a specific space time point."

"So he's telling the truth," Sheppard confirmed.

"About how he got here, yes," Rodney agreed. "As to the rest of his story? Couldn't tell you – there's nothing on the laptop about the Control Chair add-on."

"But you believe him?" Sheppard looked at Rodney in all seriousness.

"I do," Rodney said grimly. "There's no evidence to confirm it but ... this is General O'Neill ... _our_ General O'Neill. And even if it wasn't I don't think there's a universe out there where you couldn't trust him. Maybe that's why they chose him to make the trip."

"That's one of the things I intend to find out," Sheppard promised.

**Authors Note:**

I know in McKay and Mrs Miller they let Rod run around the base freely practically from the minute he got there but ... I think they should have been a little more cautious - what if he'd been 'evil' Rodney? How fun would that be? Anyways, for my foray into visitors from another universe I decided Shep would be just a little bit more cautious than that :D

You've probably guessed from this chapter that O'Neill has travelled from a future far enough away that Atlantis has moved to their new planet. I made up the time travel method because the whole solar flare thing seems inconceivable (especially since we know it happens in The Last Man). It wouldn't work if in the future they're on a different planet because my understanding is a wormhole travelling through a solar flare can only take you somewhere in time to the planet you were going to – so not the old Atlantis planet where we still are for this story. I was inspired to use the concept from McKay and Mrs Miller simply because they kept calling it "parallel space time" and I thought why not time as well as space?


	8. Okay, then where the hell was I?

**Chapter 8: Okay, then where the hell was I?**

"You believe me," O'Neill stated it like a fact, glancing quickly at each face as team Sheppard and Doctor Weir sat surrounding him in the Conference Room. It had been an hour or so since Rodney had confirmed most of the General's story and Sheppard was impatient to find out more so he could work out what to do about it.

"The science doesn't lie," Rodney confirmed briskly.

"We believe you're our General O'Neill," Sheppard clarified, "but we're still a little hazy on the Control Chair add-on. You could help with that by telling us everything you know about what went wrong."

O'Neill slouched in his chair, fingers idly turning a paper clip in an endless circle as he considered the implications. His expression was hard to read ... and he gave no obvious reaction while Sheppard was speaking.

"Don't do the whole messing with the future spiel," John continued. "If your original plan to stop us from plugging in the add-on had worked I'd understand ... but by being here you've already messed with the time line. You're gonna have to give us more than what you've offered so far for us to have any hope of fixing this."

"What do you want to know?" O'Neill finally asked, seemingly openly.

"What problems did the add-on create?" Doctor Weir asked. "If we can understand what we're up against it'll help us find a solution."

"I'm no computer expert," O'Neill quipped. "I usually leave all that stuff up to Carter."

"Sam's on Atlantis?" Rodney jumped in with a surprised look.

"See this is why it's dangerous for me to be talking to you like this," O'Neill complained in frustration, neither confirming nor denying Rodney's assumption.

"Rodney, stick to the point," Elizabeth admonished.

"He _has_ a point," Sheppard broke in with a pointed look. "How come you're the one they sent here?"

"I volunteered," O'Neill replied easily. "Besides, I'm back on Earth in this time point ... McKay thought the distance would lessen the risks of that cascade thing affecting me."

"Temporal entropic cascade failure?" Rodney quizzed.

"That'd be the one," O'Neill agreed. "Once the breadth of the problems with the city became obvious they dialled Earth and requested I come to Atlantis."

"Because aside from Colonel Sheppard you're the only recorded ATA gene holder with a natural empathy for the Control Chair," Weir deduced.

"That's right," O'Neill agreed. "They needed back up for Sheppard and it wasn't like I hadn't been to Atlantis before."

"Of course," Elizabeth said pleasantly. When O'Neill remained silent she prompted him to continue. "You were going to tell us what the problems were."

"Was I?" O'Neill held his gaze to Doctor Weirs ... she gazed back resolutely until O'Neill relented. "Fine - I'll admit that I didn't understand all the details but from what I do know it has to do with file fragmentation."

"Oh God," Rodney muttered sickly, looking at Sheppard guiltily. "I detected a problem caused by that a week ago ... I convinced Sheppard it was nothing more than a maintenance issue!"

"At first it was," O'Neill continued. "Apparently it took a _long_ time to notice anything was off. The fragmentation got so extreme that it began to seriously affect the operation of all the city systems. It also affected Colonel Sheppard's bond with the awareness of Atlantis ... eventually we lost the ability to communicate with the city on that level."

Sheppard frowned when he registered what the General had said. _O'Neill_ knew about his connection to the city? He wasn't sure whether that bothered him or not ... although he shouldn't have been surprised. In his admittedly limited experience he'd staked the outcome of an entire mission on O'Neill being very perceptive. If he'd spent any length of time in the city with John in attendance he might well have noticed enough to make his own conclusions.

"A long time?" Rodney asked in confusion. "How long is 'a long time'? And speaking of time, how far back have you travelled anyway?"

"I wouldn't call that the barest details McKay," O'Neill replied sternly. "It's not something you need to know."

"How much time we have to fix this thing _is_ something I need to know," Rodney insisted.

"Enough," O'Neill looked at Rodney with a serious expression at odds with his usual casual demeanour. "You have enough time McKay ... if you focus on finding a solution."

"I know the city being so badly affected is an issue for Earth," Sheppard mused, glossing over what O'Neill had said about losing Atlantis's awareness. "But surely that wasn't enough for the level of desperation that would prompt you to send someone back in time!"

"You're right," O'Neill's expression was grim. "Losing Atlantis was just the start of our problems. We were forced to abandon the city when we couldn't make anything work anymore. It all happened very quickly in the end ... we couldn't even dial Earth and had to retreat to the alpha site. That's when the Replicators came."

"_You didn't self destruct?_" Rodney's tone was beyond incredulous. "What the hell was I thinking?!"

"We didn't have the systems necessary to do it," O'Neill defended. "We disabled the Gate ... placed some charges at strategic locations and blew a few really big holes in the bottom of the city – sank her we hoped deep enough that no one would ever find her."

"But the Replicators did," Elizabeth said emotionlessly.

"Yeah," O'Neill grimaced uncomfortably. "They repaired everything – our damage _plus_ the damage done by that add-on device. They took the city, left the planet with a host of Replicators on board. Within days they were out there, wiping out human settlements with no resistance."

"Okay that's bad, but not as bad as it could be, unless ... tell me you destroyed the database?" Rodney begged weakly.

"Oh it gets much worse," O'Neill revealed. "The same problems that stopped us from self destructing also stopped you from unleashing the database virus. Before too long the Replicators had used the information to find Earth. You don't want to know how bad it got after that when we tried to stop them from making that trip. Suffice to say we were plenty desperate enough to try this plan. McKay and a few others holed up at an Ancient outpost the Replicators _didn't_ know about ... the rest of us held on until they were able to get the time travel system up and running. When I left the Replicators were entering orbit around Earth."

"I'm sorry General," Elizabeth said softly. "It must have been difficult to lose the city like that ... and the human cost ..."

"Yeah well hopefully you won't have to find out what that feels like," O'Neill's expression was blank, everything he'd seen and done locked tight at the back of his mind.

"Did you ever find out why the data pad malfunctioned so badly?" McKay asked. "I mean, I looked at those original schematics and the Ancients intended the add-on to be permanent. The design is relatively simple – I don't see how fragmentation can even be a side effect."

"Neither could your future self," O'Neill replied. "By the time he'd traced our problems back to that device we had systems crashing all over the place – it went from minor inconvenience to major issue pretty much overnight."

"He didn't have time to look into it any further," Rodney concluded.

"No," O'Neill agreed. "Especially after he came up with the idea to come back here and stop you from plugging it in in the first place."

"But surely I would have known there was something wrong long before things got so bad," Sheppard protested. "Atlantis would have said something ... _done_ something to cause suspicion."

"Hindsight Colonel," O'Neill countered. "Looking back it was obvious something wasn't right but ..."

"I ignored it," Sheppard finished uncomfortably. "Just like I was about to ignore it this time."

"Don't be too hard on yourself Colonel," O'Neill said casually. "Believe me when I say this - you did _everything_ you could to fix things."

"You mentioned yesterday that the future McKay had another solution," Rodney spoke up hesitantly.

"There was a subroutine he stumbled across not long before we were forced to abandon the city," O'Neill revealed. "Some kind of deep maintenance cycle ... it required someone operating the Control Chair with a strong enough gene to have access to everything and to be able to talk to Atlantis directly. McKay was pretty sure that running it would purge the effects of the add-on _and_ allow you to remove it."

"So why didn't you use it?" Sheppard asked, feeling a deep sense of foreboding – he'd asked the question but was no longer sure he really wanted to hear the answer.

"We tried once but ... things had already gone too far and then ... we didn't have a second chance," O'Neill replied like it should have been obvious.

"Wait a minute," Rodney protested. "_You_ have the gene ... I don't know whether yours trumps Sheppard's but it's stronger than anyone else we know of. How come you couldn't try it yourself?"

"Let's not start a 'mine is bigger than yours' contest," O'Neill said mockingly.

"He's right," Sheppard ignored that jibe, plus the fact that O'Neill hadn't really mentioned him. Had he been killed in battle? "How come you didn't just fix it yourself if all it required was someone to merge with the city?"

"Atlantis wouldn't talk to anyone but you despite the fact that the add-on gave us more than one option there," O'Neill replied. "I'm betting that if it's not already, within a couple of weeks the same will be true here."

"Okay, then where the hell was I?" Sheppard asked impatiently. "Because I sure as hell wouldn't have left the city if things were as bad as you say!"

"Ah, see that would be part of the problem," O'Neill admitted, not put off by John's anger. "_You_ were the one who tried to run the maintenance cycle. Like I said we'd left it too late and things went very wrong ... we couldn't disconnect you and then ..."

"Atlantis _killed_ me?" John asked incredulously.

O'Neill nodded casually, adding "If it's any consolation Rodney wasn't sure _she_ made it back from that either – he couldn't be positive though because with you gone we couldn't check."

"That's not exactly reassuring!" Sheppard shook his head grimly. "And I suppose you want me to volunteer for the same thing again?"

"You're getting to the problem much sooner than your future self," O'Neill pointed out. "My McKay was sure that would make the difference between success and ..."

"And what - death?" John interrupted heatedly. "Does this whole thing sound crazy to anyone other than me?"

"It won't come to that," O'Neill retorted impatiently.

"Well forgive me if I'm a little sceptical," Sheppard said sarcastically. "You just finished telling me that in your time it _did_ come to that!"

"Gentlemen," Elizabeth's tone warned both men that they were getting off track. "We've been at this for a while and from what General O'Neill has shared it seems at this point we _do_ have some time. We'll take a break and come back to this in an hour."

Sheppard didn't wait for any comments from anyone, jumping up and striding quickly from the room.

"Don't worry General," Elizabeth said softly. "He'll come around."

"I know," O'Neill replied. "I just hope he doesn't leave it too long this time."


	9. I should have known!

**Chapter 9: I should have known!**

Sheppard went straight from the conference room to his quarters, needing to think ... needing some help to work out what he should do next.

"Did you get most of that?" John directed his question to Atlantis, speaking aloud because he preferred it that way.

"_We did_," the chorus said simply. "_We do not feel any different ... perhaps there has been some kind of mistake._"

"There's no mistake," Sheppard insisted grimly, pacing around in the small space beside his bed. "Look at what happened with that temperature rise you thought you'd detected. And you've been ... sluggish lately ... there've been a couple of times I wasn't sure you were even hearing me."

"_Response times have been down on average 3.73 milliseconds_," Atlantis admitted.

"Do you know about the subroutine General O'Neill was alluding to?" Sheppard asked curiously.

"_Yes_," Atlantis revealed. "_There are certain things we cannot check for, despite our level of awareness and the connections between all our systems. The fragmentation Doctor McKay spoke of is one of these because to our awareness the necessary information_ is _there when we need it. Defragmentation is part of the scheduled maintenance for this reason. It would only be when fragmentation is extreme that we would notice a problem. It has been a very long time since this has occured."_

"But you've already noticed a drop in your own responses," Sheppard frowned in confusion.

"_A drop that is well within the normal range," _Atlantis countered.

"So it doesn't register as a problem," Sheppard concluded. "And if you didn't know there was something wrong you wouldn't have known to tell the future me to run this subroutine. Not exactly the most strategic back up plan there."

"_As we explained after Aperio, there have been others throughout our history that possessed the ability to communicate with us as you do," _Atlantis continued._ "It was these individuals who created and then utilised the deep maintenance subroutine ... to rejoin critical files and remove dangerous blockages within the systems. It was seen as the only efficient way to address a potentially dangerous problem._"

"Sounds simple," Sheppard quipped. "What's the catch? I know there has to be one."

"_It required such a deep level of communication because it was necessary for the operator to merge with the systems enough to literally travel mentally through every one of them_," the chorus chimed in the lower range, managing to sound almost apologetic. "_The subroutine was merely the means by which problem areas were flagged. The work of traversing the systems ... of fixing any problems rested solely on the human operator_."

"And that was a problem because ...?" Sheppard trailed off, waiting for Atlantis to finish that sentence.

"_To complete a standard deep maintenance cycle is the work of hours_," Atlantis explained. "_If our systems were as corrupted as General O'Neill suggested then by the time the subroutine was accessed fixing the problem was likely the work of days. It is very draining._"

"And I'm guessing it's not possible for the operator to just stop and take a break?" Sheppard joked.

"_No_," Atlantis replied. "_The maintenance routine will not release the operator until all the files have been repaired. Nor is it possible for anyone else to break the connection_."

"So my future self stayed connected for too long and then couldn't find his way out?" Sheppard tried to ignore the memories that tried to float to the forefront of his mind. The whole thing was starting to sound too much like his captivity inside the Aperio system – not something he was keen to even talk about let alone experience again.

"_It was always a risk during the deep maintenance cycle_," the harmony shifted with regret. "_There have been incidents in the past where the life of the human operator was threatened ... and times when they did not survive."_

"Why didn't they just change the maintenance subroutine then?" Sheppard suggested. "Made it so it didn't all have to be done at once?"

"_The original creators of the city systems never envisaged a time when the occupants would be so deeply connected_," Atlantis explained. "_The storage medium used to house and protect the systems was designed to minimize corruption ... it is these measures that make defragmentation difficult to correct. The maintenance subroutine addresses this but it must operate around the limitations imposed by the underlying design._"

"If the storage medium is designed to stop files getting corrupted, how come you've got fragmentation?" Sheppard pointed out what he saw as a flaw in that logic.

"_Minimise_," Atlantis corrected. "_It is impossible to stop file fragmentation completely, particularly for systems constantly in use. The maintenance subroutine was designed to be run infrequently ... the creators locked the coding to ensure at least those files would remain intact_."

"So the Ancients couldn't change it, even after they discovered it could kill the operator?" Sheppard tried to summarise what Atlantis had been telling him.

"_They could not," _Atlantis confirmed._ "Instead they began to pursue ways to replace the human conduit with a computer driven replacement._"

"Were they successful?" Sheppard asked, perking up at the possible reprieve if he could get his hands on the alternate system.

"_Again the project was seen as something that might put our awareness at risk_," Atlantis replied. "_We know of the location for this research however ... your team, with Doctor McKay in attendance, should be able to find out if the Ancients made any progress._"

"Thanks," Sheppard jumped up excitedly, all set to head down to Rodney immediately. Before he got to the door he stopped. "It's not that I don't want to connect with you like that," he said hesitantly. "It's just ..."

"_Your ordeal with the Aperio system followed so closely by your return to Earth still troubles you_," Atlantis finished John's statement. "_Give it no further thought John ... we understand your reluctance._"

"Okay," Sheppard got back to heading out to find Rodney, switching to thought once he'd gotten into the corridor outside his room. "_So you'll give me the gate address ... Rodney will check it out on the database and then we can come up with a plan to convince Doctor Weir we should go there_."

oOo

Sheppard filled Rodney in on what he'd found out from Atlantis and the two of them settled in to find out as much as they could before taking it to Doctor Weir. Rodney found the outpost listed in the Ancient database exactly as Atlantis had described – on a planet called Kalla. The details were sketchy but Rodney was persistent in digging as deep as possible to find out enough to convince Elizabeth they should go there.

"Why didn't the normal maintenance routines fix this?" Sheppard asked Rodney intently. He'd been thinking about everything Atlantis had said and that was the one thing that stood out.

"Ah ... good point," Rodney returned. "I don't know."

"Well make some time to look into it," Sheppard requested, his instincts telling him there was a clue there somewhere.

"I'll add it to my list," Rodney quipped, turning to his screen already distracted back to checking out the gate address Atlantis had given them.

"No," Sheppard's tone was insistent. "Make it a priority. We need to know more before we can head out to Kalla."

"Fine," Rodney said irritably. "I'll put it at the top of the list!"

oOo

"Who'd we lose?" Sheppard sat down in the commissary across from the General. It was going to take Rodney some time to finish up in the lab ... plenty of time to find out anything that would make a difference in the future.

"I knew one of you wouldn't be able to resist," O'Neill didn't answer the question. "For some reason I thought it'd be McKay."

"Yeah, well maybe he's still planning his campaign. Who'd we lose?" Sheppard looked at the General intently.

"You know I can't tell you," O'Neill replied.

"Don't give me that," Sheppard said hotly. "I _saw_ the look on your face when you greeted Elizabeth – like you hadn't seen her for a long time. Is she dead?"

"I don't live on Atlantis, remember," O'Neill said simply. "There are a lot of situations that could explain that - maybe she just got reassigned ... not everyone wanted to stay here forever like you."

"Okay – so not Elizabeth," Sheppard persisted. "Who then?"

"Anything I tell you risks altering the timeline," O'Neill said impatiently.

"Screw the timeline!" Sheppard retorted angrily. "And don't pretend you wouldn't try and take advantage of this if you were in my place!"

"Maybe," O'Neill acknowledged, "but this situation is entirely different – I've already altered the future by coming here. Anything I tell you may very well change – do you really want to be stuck living in expectation for when someone's gonna die when it might not even happen?"

"If I can save them, hell yes!" Sheppard returned.

"Okay, maybe I understand that too," O'Neill rubbed a hand over his forehead tiredly. "But I'm still not gonna tell you anything."

"But –," Sheppard started to argue again.

"Colonel," O'Neill's tone was suddenly that of a General talking to a subordinate. "We're done here."

"Fine ... _Sir_," Sheppard pushed back his chair forcefully and strode angrily from the room.

General O'Neill watched him go, sighing tiredly. He'd told Sam this kind of thing would happen – it didn't make it any easier knowing he'd been right.

oOo

Sheppard's anger carried him back down to Rodney's lab. "Forget whatever plans you had to ask O'Neill anything about the future," he said by way of greeting.

"I wasn't planning anything," Rodney denied unconvincingly, "just ... you know ... surely I've made some inroads into unifying theory by then."

"And you think _O'Neill_ will be able to tell you about them?" Sheppard's anger dropped away abruptly as he laughed at Rodney's crestfallen expression.

"Good point," Rodney agreed weakly. "So he wouldn't tell you anything?"

"Wouldn't even give me a clue," Sheppard grimaced dejectedly.

"So we're back where we would have been anyway," Rodney pointed out the obvious.

"I guess," Sheppard agreed. "Finish up here – I'll be in my office."

oOo

"Turns out your instincts about the scheduled maintenance were spot on," Rodney revealed, striding into Sheppard's office purposefully an hour later. "It was switched off deliberately ... there haven't been any maintenance runs since just after we plugged that add-on in even though on the surface it looks like there were."

"Can you fix that – turn it back on?" Sheppard asked thoughtfully.

"Not exactly, but I have managed to slow down the rate of fragmentation," Rodney said smugly. "By relocating the defrags from the scheduled code and running them manually at regular intervals I should be able to head off some of the fragmentation going on right now."

"What about the files that have already been affected?" Sheppard looked at Rodney expectantly. "Can you get it to fix those too?"

"No," Rodney admitted starkly. "This is only a stop gap that'll buy us a little more time – it's picking up some of the new fragments but there are a tonne more it can't handle. The damage that's already been done is too extreme for the standard maintenance to fix. It's pretty clever actually," Rodney said with a hint of admiration in his voice. "The device _encourages_ the systems to both fragment files into very small pieces for processing _and_ spread them a lot further throughout the system than usual. There's some pretty sophisticated programming at work here because it's been done in such a way as to convince the Atlantis systems the maintenance is still being done. While she can still access all the information there'd be no reason for Atlantis to raise the alarm."

"The Replicators!" Sheppard stood up abruptly as all the pieces shifted in his mind, forming a very worrying picture.

"Huh?" Rodney gaped at John in confusion at that abrupt interpretation.

"Think about it McKay," Sheppard insisted. "They probed my mind all those months ago but never acted on anything they found out ... as far as we knew. They focused on apparently incidental memories instead of going to the obvious like the Gate address for Earth. I _knew_ at the time there was something not right about that!"

"You think the Replicators set up this elaborate plan and then settled in to wait maybe years for it to pan out?" Rodney asked in disbelief.

"They're very patient Rodney," Sheppard replied. "And they've had no luck with a direct attack. Maybe they saw this as the only way they could defeat us. O'Neill said the Replicators came to their abandoned Atlantis soon after they sank it – how would they have known the city was even in trouble unless ..."

"Unless they set the whole thing up themselves," Rodney's face said he was starting to be convinced that Sheppard was on to something.

"The hum!" Sheppard's voice was filled with angry remorse at an unpleasant realisation. "I didn't sense it when we were on M4R 379. _I should have known!_"

"Known what?" Rodney looked at John expectantly.

"They lured us there Rodney based on what they saw in my mind!" Sheppard ground out. "They lured us to that planet and made sure we found the data pad, knowing we'd plug it in eventually."

"They want the city," Rodney said in dawning horror, "and in the future we gave it to them."

**Authors Note:**

Sorry there was no chapter yesterday ... hope this one was worth the extra days wait. Also there'll be no chapter tomorrow ... got some work things to catch up on!


	10. That wasn’t exactly quiet!

**Chapter 10: That wasn't exactly quiet!**

"This whole plan was targeted specifically at me," Sheppard's tone was bland ... inside he was struggling with the guilt at being used that way but he didn't let any of it show.

"How so?" Doctor Weir waited for John's explanation, sitting in her usual spot in the Conference Room with Team Sheppard, Carson and General O'Neill all in attendance.

"Atlantis said the project to create that add-on was developed _before_ the war with the Wraith got out of hand," Sheppard explained. "There would have been plenty of time while the Replicators had free access to the Ancient systems for them to find out about it. I don't think the Ancients ever got that project to completion - not to test it anyway ... the Replicators just made it look like they did."

"The outpost on M4R 379 wasn't an Ancient facility in terms of how long it's been there," Rodney broke in to report. "You wouldn't be able to tell from the structure itself, which isn't surprising if the Replicator's built it, but going over the readings I took of the surrounds I discovered that it was in fact fairly recently constructed. There probably _are_ Ancient ruins on that planet ... just not intact like the outpost was."

"And the off worlder who told Tomaskitous the story of your connection to the Ancestors?" Teyla looked at John worriedly.

"Probably a Replicator plant," Sheppard said simply. "He used the village legends to their advantage – gave Tom just enough to have him lure us to the planet _knowing_ McKay would pick up that energy reading. I should have known as soon as we got there it wasn't an Ancient facility."

"You should have known?" O'Neill queried sceptically.

"The city, in fact pretty much any Ancient structure we've been to that's still 'working' gives off a kind of hum that I hear up here," Sheppard pointed to his own head ruefully.

"Hey, I thought you said you got away from that when we were off world," Rodney protested irritably.

"And sometimes I do," Sheppard kept his tone bland, amused that Rodney was so troubled by his unique circumstances.

"And this time you didn't get the ... hum?" Elizabeth queried.

"No," Sheppard admitted. "Sometimes it's pretty faint – depending on the condition of the systems. This time I didn't get anything even though I should have. I just ... didn't notice at the time. Whatever it is that makes Ancient tech hum to me isn't something the Replicators can duplicate – I should have remembered that from Asuras when we first ran into the Replicators."

"But the device itself _is_ Ancient," O'Neill countered. "Future McKay was pretty clear on that."

"It is Ancient," Rodney reiterated what his future self had believed. "I don't know the sequence of events but ... the Ancients designed and then created that add-on to their own specifications and then for some reason they must have abandoned the project before trying it in a live test. Somehow the Replicators got their hands on it - maybe even before everything blew up between them and the Ancients. In any case they took that device and altered it in such a way that we wouldn't notice. It's the programming that makes the whole thing work and that's what they took advantage of ... I'm pretty much convinced that only the Replicators could have done that."

"Then we're already one step ahead this time," O'Neill said simply.

"He's right – knowing it's the Replicators should help us defeat this thing," Rodney replied.

"Have you thought any more about the maintenance subroutine?" O'Neill asked Sheppard with a significant look. "My McKay was pretty clear that there is a time limit here ... the longer you delay the less chance there is you'll be successful."

"Did more than that," Sheppard replied somewhat flippantly. "I spoke to Atlantis about it ... what she told me is consistent with what your McKay believed. It takes time for the subroutine to work through the whole system – the more problems, the more time required. The human operator has to be connected continuously, hence the greater chance for problems disconnecting."

"So we should act now," O'Neill persisted.

"Atlantis said what happened to my future self was a flaw for the Ancients too," Sheppard revealed. "They were working to resolve it. There's a planet, Kalla, where they were developing a computer driven replacement to having a human conduit for the subroutine."

"And you want to go there," Weir's statement was not a question. She glanced quickly at General O'Neill when Sheppard nodded wordlessly.

"This is on me," Sheppard directed his arguments to O'Neill, knowing he was the one he'd have to convince. "It was _my_ thoughts the Replicators used to set us up, my connection to the city they exploited. And I was too keen to make use of that add-on to the point that I ignored some pretty obvious clues that were there _before_ we even plugged it in," he paused as the others considered what he'd said. "Don't get me wrong - I _like_ being able to talk to Atlantis but ... it comes at a cost. The thought that others could talk to Atlantis too, that it wouldn't all rest on me? If I'm honest, in the end that was pretty much the only thing driving me."

"And you think whatever's on Kalla will undo that?" O'Neill asked.

"We need something that's gonna fix this permanently," Sheppard stated firmly. "And it's not about taking the pressure off me anymore – it's about removing the current vulnerability so that something like this can't happen again. If it doesn't pan out I can still do the subroutine myself."

General O'Neill looked at Sheppard assessingly for several moments before nodding imperceptibly.

"Ready your team," Elizabeth agreed.

oOo

Kalla was a planet that looked a lot like every other place they'd been to in the Pegasus galaxy, especially the usual trees that provided cover around the Gate but also obscured the view of any possible dangers. The MALP they'd sent through first hadn't detected anything of concern but Sheppard always preferred to confirm these things with his own eyes ... with a little bit of help from the Ancients of course.

"You detecting any life signs?" he asked Rodney, taking the Jumper into a high arc away from the Gate.

"None within scanning range," Rodney replied.

"Energy readings?" Sheppard looked at Rodney hopefully.

"Not so far," Rodney reported, "although if this planet is like most of the others the really good stuff will be located a fair way from the Gate."

"Okay – so we do this the hard way," Sheppard drawled, calling up the HUD. "We'll sweep the planet looking for any kind of structure ... hopefully we won't have to resort to searching on foot."

A couple of hours later Sheppard was ready to call this one another bust ... they'd covered most of the planet in a high search pattern and found nothing. Reluctantly turning the Jumper back towards the Gate a small flashing dot on the HUD drew his attention.

"We've got something, dead ahead," he revealed. "It's a little hard to tell but I think it's some kind of building."

"Why did we not detect it on our first pass?" Teyla queried.

"It's in a valley hidden by the forest," Sheppard brought up a different view on the HUD to show the others the topography of the surrounding area. "We're gonna have to walk."

"Great," Rodney complained. "That's just what I need ... a long trek through a dingy forest to a place that will probably contain nothing."

"Stop complaining McKay," Sheppard ordered, landing the Jumper in a small clearing as close to the building as he could get.

"You do realise the chances we'll find anything in that building are less than slim, right?" Rodney retorted sarcastically. "We're in range and I've got nothing ... which means that building's not putting out enough energy to power a flash light."

"Gear up," Sheppard ignored Rodney's lack of enthusiasm, clipping on his P90 before opening the back of the Jumper.

"Rodney may be right John," Teyla warned. "There is no guarantee the Ancients did anything with the project Atlantis told you about. The city records can only cover events that took place within the city itself."

"Unless the Ancients returned and updated the records," Sheppard replied. When Teyla frowned at his attitude he relented. "Look I know this is a long shot okay. But we still have to follow it up before we fall back to O'Neill's plan."

"You're not actually gonna do that maintenance meld are you?" Rodney asked worriedly. "After what General O'Neill said about what happened in his time?"

"Hopefully it won't come to that," Sheppard dismissed the subject abruptly, cloaking the Jumper before starting the long walk. "Everyone remember where we parked," he quipped.

"Great - you're stealing lines from Star Trek now?" Rodney protested, letting himself be distracted.

"You're one to talk Rodney – didn't you want to rename our Ancient ship Enterprise instead of the Orion?" Sheppard reminded him.

"That is a perfectly good name for a space ship," Rodney defended.

"Well, in the famous words of another science geek, I know you love scanning for life forms so get started," Sheppard grinned when Rodney rolled his eyes at that one, Teyla and Ronon looking on with obvious confusion. "It's from a movie," Sheppard said apologetically. "Probably not one you've seen though so I probably shouldn't have ...," he trailed off lamely. "You picking anything up McKay?"

"Surprisingly no," Rodney replied sarcastically.

"Well keep looking," Sheppard picked up the pace, quickly putting himself in the lead position.

The forest was dense making visibility poor which made Sheppard wary and even more on guard than usual. Something cracked to his right – Rodney yelped, dropping his scanner and then fumbling around on the ground to pick it up. Sheppard listened for a few moments before relaxing.

"Sorry," Rodney glanced around nervously, clearly expecting bad guys to jump out at them at any moment ... even though his scanner said no one was around.

"Probably some kind of small animal," Ronon offered that explanation casually. Sheppard nodded, motioning for them to continue forward.

Rodney kept up a steady stream of nervous chatter as they walked through the forest. Half an hour later they spotted something obscured by the trees ahead ... a flash of colour and edges inconsistent with the surroundings. Sheppard motioned abruptly for Rodney to be quiet ... a few more cautious steps forward revealed that it _was_ the building they were interested in.

The forest was such that a dozen enemies could be lying in wait and they wouldn't know it ... by the same reckoning though Team Sheppard were able to get pretty close to their target without fear of their presence being detected.

"Can you tell what's in there?" Sheppard asked in a low voice.

"It's shielded," Rodney said in an incredulous whisper. "There could be a swarm of Wraith in there and we wouldn't know it."

"If we open the door a little, will you be able to scan inside?" Sheppard queried.

"Maybe," Rodney replied.

"Good enough for me," Ronon jumped up and sprinted the few remaining metres to the door.

"_Quietly_," Sheppard ordered in a harsh whisper. "We don't want to alert whoever might be in there to our presence."

Ronon did a thumbs up in understanding, before pulling out his blaster and firing a single shot at the locking mechanism. When the smoke cleared it revealed the door now standing ajar, edges blackened from the blast. Sheppard motioned for Teyla and Rodney to follow him as they ran to join Ronon.

"That wasn't exactly quiet!" he glared at Ronon irritably.

Ronon shrugged without remorse, turning back to Rodney curiously. "Getting anything now McKay?"

Rodney had been focused on his scanner from the instant the door had opened. Now he looked at Sheppard with a horrified expression. "I'm picking up multiple signals ... they're Replicators."

**Authors Note:**

Please excuse my silly references to Star Trek The Voyage Home ('remember where we parked') and Star Trek Generations ('I just love scanning for life forms ... life forms ... you tiny little life forms ...') - couldn't resist and I can just imagine Shep doing that deliberately to distract Rodney away from stuff he doesn't want to talk about!


	11. It’s an all or nothing thing

**Chapter 11: It's an all or nothing thing**

"How many?" Sheppard demanded.

"_Too many_," Rodney retorted, "I don't know – twenty, maybe more?"

"Fall back," Sheppard pushed away from the door, covering the opening while the rest of his team moved silently back into the cover of trees before he joined them.

"If you are thinking we can somehow overcome them I would advise against it," Teyla looked at Sheppard sternly. "There are many more Replicators than we could handle even with the ARG weapons - which we do not have."

"Teyla's right," Ronon agreed. "Whatever was in that building is as good as gone anyway."

"The Replicators knew about the intended addition of communication capability to the Control Chair," Rodney said weakly. "It stands to reason they'd know about this place too. I'm sorry ... I should have thought of that _before_ we came here."

"Wouldn't have mattered McKay," Sheppard finally spoke up, his face carefully blank as he gazed at the still open doorway. "We still would have come here to check it out ... at least we know there's no help coming from this angle."

"We need to get out of here," Rodney urged nervously. "It won't be long before the Replicators turn up to see why it's getting drafty in there – once they see Ronon's handy work they'll know we're here."

"Okay, back to the Jumper," Sheppard jumped up and started running back the way they'd come. "Try to keep up McKay."

oOo

"The Replicators got there first?" Elizabeth looked around the conference room table as Team Sheppard made their report on the failed mission to her and General O'Neill.

"They would have known about the project to dehumanise the deep maintenance cycle," Rodney explained. "I guess they wanted to cut off any chance of us fixing the problems they've created ... you know, covering their bases in case we got to the point of working out what they'd done."

"Okay I'll do it," Sheppard had been strangely quiet while the rest of his team filled the others in. Now he spoke up abruptly, drawing all eyes to him.

"Huh?" Rodney looked at Sheppard in confusion.

"I'll do the maintenance subroutine thing," Sheppard clarified. "But I need to speak with the city first, find out how it's all supposed to work. Just ... talk amongst yourselves until I get back." Not waiting for any protests he turned and walked hurriedly from the room.

Rodney turned back to Elizabeth in concern. "You're not gonna let him do this are you – knowing what happened in the future?"

"It's his choice Rodney," Elizabeth replied, keeping her personal feelings very much hidden.

"Yeah but I haven't even had a chance to explore other solutions yet," Rodney protested. "Maybe I can write some kind of program to defrag the systems myself."

"That's exactly what you thought in the future too," General O'Neill said almost gently. "You ran out of time."

"Oh," Rodney sat back in confusion. "What about – "

"You tried that too," O'Neill interrupted before Rodney could finish his sentence.

"You don't even know what I was gonna say," Rodney bit back irritably.

"Doesn't matter McKay," O'Neill retorted. "Your future self has advanced understanding of the Ancient systems from where you are now ... even with that he couldn't come up with a solution."

"Yeah but this time I know it was the Replicators," Rodney said defensively. "That should open up a whole host of new ideas."

"You may not have known it was Replicators in my time, "O'Neill countered, "but you still tried a number of ideas using information you stole from them. You couldn't fix it then and ..."

"It stands to reason I'm not going to now," Rodney finished weakly.

"The only thing we can do is get Sheppard into the systems early enough," O'Neill said starkly. "You said it yourself ... or you will. It's the only way we're gonna fix this."

"Sometimes I hate it when I'm right," Rodney quipped unhappily.

oOo

"The Replicators took over the outpost on Kalla," Sheppard explained to Atlantis, once again back in his quarters for a private chat. "The automated approach is a no go so we're gonna have to do this the old fashioned way."

"_You are willing to undertake the deep maintenance cycle?_" Atlantis chorused in surprise.

"I am," Sheppard agreed, "but before I do I need you to tell me more about what to expect. I also need you to agree that you'll let General O'Neill take over – that you'll talk to him willingly – if it becomes necessary."

"_It will not become necessary_," the tones ramped up to the high pitched end in protest at the meaning behind that.

"Let's hope not," Sheppard said simply. "But I can't go into this unless I know there's a back up plan, so ..." he trailed off, waiting for the agreement he needed.

"_We will do as you ask_," Atlantis chorused solemnly.

"Good," Sheppard said decisively. "Now tell me everything I need to know about this deep maintenance cycle. And don't sugar coat it – I want to know about all the risks _and_ the worst case scenario."

"_If you are willing I can do more than just tell you – I can show you_," Atlantis dropped that bombshell out of nowhere.

"Show me?" Sheppard frowned in confusion. "How?"

"_If you give your visual perception over to me I can recreate past events in such a way as to allow you to observe them personally_," the chorus explained. "_In that way you can experience for yourself every aspect of the deep maintenance process_."

"Ah," Sheppard hesitated before nodding firmly. "Okay ... what do I have to do?"

"_Close your eyes and relax your mind_," the chorus shifted through the normal range of sounds. Sheppard found himself caught up in their harmony, mesmerized by the shift and play of notes inside his head.

And then he was no longer inside his head ... he was standing in the Control Room, the familiar almost Grandmotherly figure of Atlantis standing beside him.

"Where are we?" John looked around curiously, strangely untroubled by the fact that he was having an apparent out of body experience.

"These events took place approximately one hundred years before the war with the Wraith," Atlantis replied. "The two people you see before you are Herous and Lalita, the current leaders of the city. I brought you here first so that you could hear their conversation ... fragmentation within the systems has escalated and it will be Lalita who will need to perform the deep maintenance cycle."

Sheppard turned back to the couple, ready to eavesdrop on their private conversation.

"Do you forget what happened last time?" Herous whispered urgently. "It almost killed you!"

"This time will be different," Lalita replied. "I allowed myself to get entwined within the systems beyond what was necessary. And yet I did break away before it was too late."

"You could have been stuck inside those systems forever," Herous said angrily. "If you'd been connected any longer you wouldn't have _wanted_ to break free. You know the doctors can't disconnect you while you're operating the chair."

"You worry too much," Lalita put a hand on Herous's arm.

"And you don't worry enough," Herous retorted.

"I will be fine," Lalita smiled confidently. "This time I have the experiences of last time to draw on. All will be well."

Atlantis drew John away from the scene, steering him down the stairs and across the Gateroom with a hand on his elbow.

"What happened to her?" John asked curiously, taking in the sights of a fully occupied and somehow youthful Atlantis with interest.

"She completed the maintenance cycle without incident," Atlantis replied. "And did so again many times in her lifetime."

"Okay, so what next?" John glanced at Atlantis expectantly.

"The Control Chair," Atlantis said simply. The air around them pulsed and they found themselves standing inside the Chair Room. The Chair was occupied by a young Lantean male, deathly pale and motionless. Beside him stood an older couple who could only be his parents. Their arms were around each other as they watched their son in torment.

"Make it stop," the woman begged. "Make him return to us."

"He is too deeply immersed in the systems," the man ground out. "He has been lured by the freedom his mind enjoys ... he will not be torn away from that."

"You said it would be all right," the woman broke away and glared at him accusingly. "_You said_ the modifications you made would ensure that no one would be lost like this again." Not waiting for a response she ran from the room, her sobs echoing from the corridor as she disappeared from sight.

The man turned back to his son, kneeling beside the chair and putting a hand on his cheek. The air pulsed again ... John and Atlantis were still in the Chair Room but it was no longer occupied.

"What happened?" John felt disturbed and uncomfortable with the scene he'd just witnessed.

"On rare occasions the initiator of the maintenance cycle became ... addicted to the thrill of complete mental freedom," Atlantis explained. "It happened most often during cycles of unusual length or complexity. They chose to leave their bodies behind, merging their consciousness with the city."

"So they died," John said starkly.

"For all intents and purposes yes," Atlantis agreed, "although their essence, their memories, a small part of who they were remains within the systems to this day."

"That guy's father tried to prevent it?" John queried.

"He tried to insert an additional step at the beginning of the coding, hoping to limit the length of the cycle," Atlantis revealed. "He thought the cycle could be run in stages, allowing the operator to rest and recover between each."

"But it didn't work," John stated.

"No," Atlantis said sadly. "As I said before, the maintenance cycle coding was locked by its creators. Attempts to circumvent this by adding coding around the subroutine always failed ... the original directive to complete the entire cycle before releasing the operator still remains intact."

"It's an all or nothing thing," John summarised. He looked at the Control Chair blankly, his mind engaged in processing what he'd just seen. "Anything else?"

"There is one more thing I would like to show you," Atlantis replied, making the air shiver around him one final time. Expecting to see the Chair Room again John looked around in confused surprise. Around him were brightly lit conduits crisscrossing and zigzagging in all directions. Ancient symbols hung in the air, some scrolling rapidly, others flashing irregularly, still others pulsing strongly. There were shapes surrounding him too – ghostly outlines of walls and doors, control consoles and display screens – all there together and overlaid as though he could see through the walls and perceive the entire structure and content of the city in a single layer. He had to be looking at Atlantis from the inside out!

"Are we where I think we are?" John asked in amazement.

"Inside my systems," Atlantis confirmed. "I felt it prudent to show you what your mind will be confronted with once you've made the connection to the maintenance subroutine. You must follow every conduit, open every door, and locate components that look like this," Atlantis drew his attention to some of the Ancient text contained within what looked remarkably like the pockets you'd find on the back of a pair of jeans. "The subroutine will place markers on like components, allowing you to collect them until you have an entire file. You will then have to join the pieces together and return the restored file back to the storage medium," Atlantis showed John a circular doorway what shimmered like an open wormhole. "The subroutine will guide you through the process but it is you who will have to do all the work of gathering, joining and transporting. You will know when the cycle is complete ... the subroutine will open a doorway to release you."

"That's a lot more ... physical than I was expecting," John quipped, "but I think I can handle it."

"You must rest and prepare yourself for what is to come," Sheppard's vision flashed and he found himself back in his quarters inside his own head once more. "_Sleep_," the chorus crooned.

Sheppard knew he should report to the others, let them know he was resolved to go through with this but ... Atlantis drew a blanket of tiredness over him. Stretching out on his bed Sheppard dropped immediately into a deep sleep.

**Authors Note:**

I'm doing an early update from work today (gotta do my tax tonight - happy happy joy joy) so apologies for not replying to reviews first - can't do that from work as they won't let me log into email - I'm surprised I get to do fanfiction stuff from here actually so I shouldn't complain! I will still respond when I get a chance but thanks to everyone who reviewed since the last post. Hope you enjoy this latest installment.


	12. We will not talk to you!

**Chapter 12: We will not talk to you!**

Back in the conference room everything that could be said _had _been and so the meeting quickly disbanded, each person assuming Sheppard would call them all back once he'd done what he needed to. When he didn't it was Rodney with his typical impatience who broke first. He'd been hoping to get Sheppard alone to talk some sense into him only to be thwarted when John remained out of circulation.

"Sheppard?" Rodney stood outside John's room a few hours later. He'd checked everywhere else with no luck and John wasn't answering his radio – the only place left was his quarters. "Colonel!"

When there was still no response Rodney overrode the locking controls and walked hesitantly into the room. "Sheppard?" he called, spotting the outline of someone stretched out on the bed in the semi darkness, buried face down in the pillows. Surely Sheppard couldn't sleep through the amount of noise Rodney was making?

Walking over hesitantly Rodney put a hand on John's shoulder and shook it gently ... and then more vigorously when nothing happened. Frowning worriedly now, Rodney managed to manoeuvre the sleeping man enough to reveal the face of an apparently unconscious John Sheppard ... although the strong pulse he found when he checked did make him feel marginally better.

"Carson," Rodney radioed the doctor urgently. "Something's wrong with Sheppard. I'm in his quarters – you need to get down here right now."

oOo

"He's sleeping Rodney," Carson spoke softly, even though nothing he'd done so far had made Sheppard stir.

"_That's it?_" Rodney asked in amazement, watching Sheppard lying motionless on the infirmary bed. "He just decided to take a really long nap ... in the middle of the day?"

"I've done every scan we have available Rodney," Carson replied insistently. "His brain activity is consistent with someone in REM sleep."

"Okay, then wake him up," Rodney waved a hand between Carson and Sheppard's bed. "If he's just asleep then you should be able to wake him up right?"

"I could do that Rodney but I don't think it'd be wise," Carson disagreed. "There's nothing physically wrong with him. All indications are that Colonel Sheppard will wake up on his own ... when he's ready."

"Fine. Maybe I'll just you know ... hang around for a bit," Rodney suggested, glancing up just in time to see the amused look on Carson's face. "What?"

"Nothing Rodney," Carson replied. "It's probably going to be a while before the Colonel wakes up ... there's no point in you waiting it out here."

"You're sure there's nothing wrong with him?" Rodney double checked, past experience with a 'fine' Sheppard who turned out _not_ to be fine at the forefront of his mind.

"Yes Rodney," Carson said in that slightly aggrieved tone he only used with Rodney.

"Okay then. I'll just go and ... you know," Rodney glanced a final time at Sheppard before leaving him in Carson's care.

oOo

'When Sheppard was ready' turned out to be a full 24 hours later. He came slowly to wakefulness, frowning in confusion to find himself in the infirmary.

"Doc?" he called out, waiting impatiently until Carson arrived at his bedside.

"Ah Colonel, you're awake," Carson greeted him with a smile.

"Yeah," Sheppard looked at him expectantly. "I'm a bit confused though – how come I'm here when I distinctly remember going to sleep in my room?"

"Rodney got concerned when you didn't answer your radio," Carson explained. "We transferred you down here because we couldn't wake you without medical intervention."

"Oh," Sheppard ran a hand through his hair as he processed that. "It was Atlantis ... she thought I needed the rest before ... you know," John waved a hand vaguely in the air.

"Well all your scans confirm you were simply sleeping," Carson replied lightly. "How are you feeling lad?"

"I'm fine," Sheppard said insistenly, swinging his legs over the edge of the infirmary bed. "Can I get out of here now?"

"I can't see why not," Carson agreed. "Just make sure you eat a good meal _before_ you return to duty."

"That'll be my second stop," Sheppard agreed.

oOo

"You're up! Carson was supposed to tell me when that happened," Rodney complained, the first to welcome Sheppard back to the land of the awake. "What was that all about anyway?"

"What was _what_ all about?" Sheppard asked in confusion. He'd stopped off at his quarters to get cleaned up and was now on his way to the commissary as promised ... he'd almost made it too - before literally bumping into McKay in the corridor.

"The 24 hours of sleep" Rodney fell into step beside him, frowning when Sheppard looked back at him blankly. "You did know you slept through a whole day right?"

"I did?" Sheppard rubbed a hand over his freshly shaven jaw. "That would explain the beard."

"So what was that all about?" Rodney returned to his original question.

"I guess Atlantis decided I needed the rest," Sheppard explained casually, "before I do this maintenance thing."

"Makes sense," Rodney's expression said he really wanted to talk about that some more but John wasn't up for it.

"In fact I'm starving too," Sheppard glanced over at Rodney, his eyes begging the other man to let it go for the moment. "I'm gonna go load up – wanna join me?"

"It's lunch time ... I could eat," Rodney replied, following Sheppard to the commissary.

oOo

"Hey – you're awake!" Ronon greeted John from their usual table with a grin.

"Way to state the obvious," Rodney muttered, throwing himself down in the chair across from Teyla.

"It is good to see you are well," Teyla told Sheppard graciously.

"Yeah – that was some sleeping pill huh?" Sheppard sat down and began to dig into the contents of his loaded tray.

"So I guess you really are hungry then?" Rodney looked on in fascination at the sight of Sheppard consuming more food than he'd ever seen him do.

"Atlantis made it clear this thing's gonna drain a lot of energy," Sheppard explained. "I just thought the more I can store up beforehand the better."

Rodney remained quiet while they all ate, even giving Sheppard plenty of time to finish most of his meal. Eventually he couldn't hold it in any more, determined to talk about what John was intending.

"Before you start McKay," Sheppard beat him to the punch, "there's nothing you can say that's gonna convince me not to do this."

"But," Rodney spluttered, taking a deep breath in preparation for lauching his arguments anyway.

"What Rodney is attempting to say is that we are all concerned about you John," Teyla broke in, levelling a stern look Rodney's way. "Particularly given what General O'Neill has revealed about the future."

"I appreciate that but things will be different this time," Sheppard said confidently. "Don't worry about it."

"So you tell us not to worry about you and what ... we don't? Like that ever worked!" Rodney said sarcastically. When Teyla sent another reproachful look his way Rodney rolled his eyes in exasperation before visibly letting it go. "Fine - we won't talk about it. There is something else though ... I was thinking about how we're gonna remove the add-on once you've completed the maintenance cycle and I don't think it'll be as easy as just pulling it out. We might need to do a complete shutdown and reset the entire system – not just the Chair - before we can unplug it."

"Won't that have an impact on Atlantis – that's why we didn't do it to get rid of Aperio?" Sheppard reminded Rodney.

"I should be able to create a safe zone," Rodney suggested. "Atlantis can wait it out there until we unplug the device and restart everything ... then she just comes back and we're all good."

"You make it sound easy McKay," Sheppard said irritably. "I can't see how you can protect Atlantis when she's still essentially part of the system."

"It was the whole Aperio thing that gave me the idea actually," Rodney said smugly. "While we don't have another portable storage device I can turn a section of the systems into one using what I learned from trapping Aperio, with its own power source to protect the contents. You just have to get Atlantis to agree to go there before you ... you know, do your thing."

"Atlantis doesn't have an active part in running the subroutine," Sheppard offered, "so it shouldn't be a problem."

"You were able to learn more from Atlantis about what to expect? Teyla asked curiously.

"Like you wouldn't believe!" Sheppard looked at each of his team in turn before continuing. "She showed me the past ... Atlantis when they used to run this thing on a regular basis."

"You travelled back in time?" Rodney asked incredulously.

"Of course not McKay," Sheppard said exasperatedly. "She took my mind on a little journey so I could see it all personally. I know what to expect now."

"So it's not dangerous after all?" Ronon asked.

"Oh it's still dangerous," Sheppard admitted. "And there's not a lot we can do to make this any easier ... but I've got a better chance knowing what's in store for me once I activate that subroutine. You guys finished?" He looked down at his own empty tray, picking up his juice and draining it in one go. When the others nodded in assent he rose. "Then we need to go and report to Elizabeth and General O'Neill."

oOo

Sheppard filled everyone in on the specifics of what he'd been shown by Atlantis, only leaving out the bit about the dangers of getting stuck – not just from being connected too long which they already knew about but also from being seduced by the experience itself. There was nothing any of them could do about that and he wasn't going to change his mind so why worry them? Knowing that Teyla and probably Rodney too would give him grief later on for keeping it from them didn't make Sheppard any less inclined to at least _try_ and make this a little easier on everyone.

"Will we be able to track your progress inside the subroutine?" Elizabeth asked.

"I don't know," Sheppard admitted. "I'll check," he added, turning his thoughts internally. "_Can you set up something for Rodney so he can keep track of me once I'm in?_"

He waited but there was no response. "_Atlantis_?" Sheppard called out in his head again. "_You there?_"

"_Who are you?_" the chorus sounded weird ... discordant and somehow frightened.

"What do you mean who am I?" Sheppard spoke aloud in his surprise, oblivious to the suddenly concerned looks of everyone in the room.

"_We do not know you_," the chorus trembled nervously. "_We sense you but our reality is blurry, strange ... why can we not see you?_"

"_You don't know who you are?_" Sheppard demanded internally, his stomach clenching at the thought that Atlantis had been damaged by the ongoing fragmentation while he'd been busy sleeping. "_You're the awareness of this city – the harmony of all its systems._"

"_YOU LIE_," the chorus cried out sharply, making him wince. "_We will not talk to you!_"

Sheppard felt the wrench in his head, the sensation of rushing motion accompanied by overwhelming fear. And then he felt nothing.


	13. We don’t know that for sure

**Chapter 13: We don't know that for sure**

Sheppard came back to himself quickly, shaking off the hands that were trying to help him up from where he'd fallen. O'Neill had remained seated but the rest of his team _and_ Elizabeth must have jumped to his aid before he'd even hit the floor.

"_I'm okay,_" he said irritably, getting to his feet and only stumbling slightly as he slumped back into his chair.

"John," Elizabeth's tone made it clear she expected the truth about his condition.

"No damage done," Sheppard said simply, making eye contact with each of the others as they returned to their seats.

"What the hell was that?" O'Neill demanded, leaning back in his chair and practically glaring at Sheppard as though he were at fault.

"Atlantis having a panic attack," Sheppard replied, rubbing a hand over his eyes in an effort to alleviate the throbbing headache he now had.

"Atlantis didn't know you?" Rodney looked at Sheppard in confusion.

"She didn't," Sheppard admitted, "but worse than that she didn't know herself either."

"This is bad," Rodney muttered weakly.

"Ya think?!" O'Neill shook his head at that one, turning to Sheppard intently. "What does this mean for you running the subroutine?"

"Probably nothing," Sheppard replied. "Only that I should do this sooner rather than later. The fragmentation must have escalated a lot while I was ... out of it. You mentioned the awareness of Atlantis," Sheppard said to O'Neill. "Did this happen in your time too?"

"No," O'Neill revealed. "Atlantis was there with you right up until the end."

"So we've changed things already, somehow made it worse?" Sheppard looked disturbed by that thought.

"Not necessarily," Rodney contradicted that conclusion. "By adding the manual defrags I may have altered which files are being split up - it's pretty random so even if I did the same thing in the future it wouldn't necessarily have the same effect. Maybe Atlantis was just unlucky this time and the files that assist her self awareness got fragmented ahead of other less critical ones."

"You don't need Atlantis to help you?" Elizabeth asked Sheppard curiously.

"It'd be nice if she was there at the beginning," Sheppard explained, "but it was pretty clear the actual work is a solo deal – she won't be able to assist me once I've started."

"Running the subroutine _might_ fix whatever's wrong with Atlantis," Rodney offered uncertainly ... he didn't understand from a scientific point of view how Atlantis could have a voice in the first place. Speculating on how to fix it would be guessing based on little more than his hopes that what he said would turn out to be true.

"And it might not," Sheppard retorted, distracted by his troubling thoughts. "I could do something though ... once I'm inside the system."

"Your first priority is fixing the problems caused by the Replicator programs so McKay can remove the add-on," O'Neill countered. "Once that's done, if it turns out Atlantis is still ... missing, you can go back in and do something about it then."

"Ah, not exactly," Rodney said weakly. "We won't be able to just pull the add-on ... we need a total systems shut down and reset first. If Atlantis, the awareness Sheppard communicates with, isn't inside the safe zone I'm going to create by the time he's finished, that process will almost certainly destroy her."

"We can't afford to hesitate once the cycle is complete," O'Neill insisted. "McKay from my time proved that our Sheppard fixed some of the files before he died ... it didn't make a difference because with that add-on still plugged in any ground we gained was lost faster than the first time."

"Atlantis is damaged because of me," Sheppard said angrily. "It all comes back to me being too keen to replace myself as the only person who could talk to her."

"You have a responsibility to _everyone_ in this city – you know what's right. Don't let guilt be the only thing driving you Colonel," O'Neill cautioned grimly.

Sheppard looked like he wanted to argue the point but somehow he managed to hold his silence, aware that everyone was looking at him expecting ... something.

"When will you be ready with that safe zone Rodney?" Elizabeth asked after a few moments silence.

"A couple of hours?" Rodney suggested, glancing at Sheppard quickly before looking back to Elizabeth. "Should I ...?"

"That should be your priority for now," Elizabeth agreed. "John, make whatever preparations you have to. As soon as Rodney's ready you'll have one final change to try to communicate with Atlantis and get her to transfer to Rodney's safe zone. If you're unsuccessful then I'm sorry ... knowing what happens in the future ... we can't afford to hesitate. You'll need to see the maintenance cycle to it's conclusion and then allow Rodney to reset all the systems."

"Understood," Sheppard's face was blank. Not waiting for anyone to call the meeting closed he rose and walked quickly and silently from the room. Rodney muttered an apology before rushing out after him.

oOo

"Is there anything you can do Rodney?" Sheppard asked quietly. Rodney had caught up with him before he'd gotten half way down the corridor and the two of them had walked the rest of the way to Rodney's lab together.

"You know I don't understand how there can be an Atlantis for you to talk to," Rodney admitted reluctantly. "There's no way to test anything I could suggest and ...," he trailed off miserably.

"There's not enough time," Sheppard concluded.

"Not really," Rodney agreed. "You might get lucky though – when you're in there rejoining all those files. I'll do everything I can to help you find the safe zone just in case you stumble across Atlantis."

"Thanks Rodney," Sheppard sat back, staring into space.

"You okay?" Rodney was uncomfortable taking the conversation to a personal level but John was his friend ... and he was potentially losing something the rest of them couldn't really even understand.

"I will be," Sheppard seemed to visibly shake himself, blinking in a deliberate manner before turning an intent gaze on Rodney. "Get done here as quickly as you can and then meet me in the Chair Room. You need to set up some monitoring equipment so you can get some kind of indicator on my progress once we get started."

"Ah, okay," Rodney frowned at Sheppard's abrupt shift in mood. He knew John Sheppard and there was no way he would just give up on saving Atlantis. Rodney was sure he was planning something ... he just didn't know what.

oOo

"Teyla, got a minute?" Sheppard stood uncertainly in the doorway of the gym where Teyla was finishing up a solo practice session. He'd turned it over and over in his head for the last hour and realised he'd have to share the full story with someone ... in the end Teyla was the only suitable candidate.

"Of course John," Teyla looked at him with concern, waiting silently as John walked fully into the room but then hesitated to speak.

"There was a small part of what Atlantis showed me from the past that I didn't tell everyone," Sheppard finally began after a few moments pause. "Sometimes the operator got stuck inside the systems just like my future self only ... it wasn't an accident."

"I do not understand," Teyla said with a frown. "How would they get stuck if not by accident?"

"They _chose_ to remain inside the systems," Sheppard admitted quietly. "The way Atlantis described it having so much mental freedom was intoxicating ... maybe even addictive. Some of the Ancients completed the subroutine so they _could_ have returned to themselves but ... they deliberately stayed there."

"They chose to die?" Teyla's expression was appalled at the very thought.

"I guess so," Sheppard agreed, "although I don't think they saw it that way."

"And you are telling me this now because?" Teyla raised an eyebrow at Sheppard expectantly.

"The risks of being lured into the systems like that were greater the more complex the damage," Sheppard explained. "Assuming our problems are gonna be at the high end of complex I need you to do something for me. If I can't complete this we still have O'Neill - he's got a strong ATA gene, he could finish it. But it'll fall to Rodney to do the hard part - to react quickly enough that he gets me out of there and O'Neill in before we loose ground. He may not have time to ... react to me not making it."

"You want me to help Rodney should it be necessary?" Teyla's face was deliberately blank as she registered what John was asking of her.

"Look - this is just worse case scenario stuff here," Sheppard said insistently. "It won't come to that but I'd be a poor leader if I didn't take care of the back up plan. Rodney will know what to do but ..." Sheppard trailed off uncertainly.

"But he will need support to see it through," Teyla finished graciously. When Sheppard nodded without saying more Teyla closed the few steps separating them and stood looking up at him intently. "I will do as you ask," she finally decided. "But should I find that you _let_ yourself be lured in such a manner I _will_ find some way to make you wish that you had not."

"I'll be fine," Sheppard insisted, trying for that boyish smile that usually worked in smoothing his way.

"You are strong ... and you will not be alone," Teyla took Sheppard's hands and drew him down to her until they touched foreheads in the traditional Athosian way. After a moment that settled a strange peacefulness over him Sheppard straightened up and took a step back.

"Thanks Teyla," he said gratefully. "I have a couple of things to get sorted and Rodney still needs to test some monitoring equipment so ..."

"I will be there when it is time," Teyla promised.

oOo

"You brought Carson?" Sheppard asked incredulously when he turned up in the Chair Room a couple of hours later. "No offence Doc."

"None taken lad," Carson replied, skirting around the Control Chair uneasily.

"Carson wanted to talk to you about setting up something to help you once you're in there," Rodney was completely unrepentant about going over Sheppard's head and bringing someone else in. He dropped down at the back of the Chair and started connecting his laptop into the system. "I've written a couple of programs to monitor the level of fragmentation – hopefully that will be enough for us to see where you're at."

"Sounds good Rodney," Sheppard acknowledged. He turned to Carson with a frown. "You know it wasn't just the future me - there were Ancients who died running this thing too," Sheppard began. "That was in a time when they were making full use of every available medical tool in this city. They couldn't protect the operator by any artificial means and I don't think you'll be able to either."

"We can't know that for sure lad," Carson protested. "At the very least I can set up a peripheral IV line – run a saline solution to stop you from getting dehydrated. We can alternate with a dextrose mixture if your blood sugar gets low."

"That might help my physical condition," Sheppard agreed, "but Atlantis made it pretty clear Carson. You won't be able to break the mental connection through any kind of medical means – not without killing me. Once I start this the only way out is to finish the cycle or ...," he trailed off without completing that statement, knowing all of them were aware of the stakes.

"This is sounding more and more insane by the second," Rodney complained bitterly. "It's not too late to change your mind you know. I know I can fix this if given enough time."

"I have to do this Rodney," Sheppard said with an easy smile. "You know there's no other way."

"Yeah but I don't have to like it," Rodney muttered childishly. "Have you tried communicating with Atlantis again?"

"Yeah, coupla times," Sheppard admitted. "She's there somewhere ... I'm still getting the usual hum but ... she's not responding. I don't know if she can even hear me where she's retreated to."

"Oh," Rodney said glumly. "There's still time so maybe ..."

"Is the safe zone ready?" Sheppard switched topic abruptly.

"Yes," Rodney grabbed his laptop and tapped a few keys, turning the screen so Sheppard could see his display. "I put it next to the systems that control the ZedPM ... it's the greatest concentration of energy anywhere in the system. Hopefully that will stand out like a bright shiny beacon amidst everything else in there."

"So all I have to do is head for the light?" Sheppard joked.

"Ha ha," Rodney was less than amused. "Hopefully if you find Atlantis you'll be able to convince her to go to the safe zone even if she still doesn't recognise you."

"Thanks Rodney," Sheppard said gratefully. "Listen, if I don't make it out of this," he began.

"Oh please," Rodney backed away, holding up his hands as if to ward off something evil. "Let's not do this!"

"McKay!" Sheppard said insistently. "I need you to pay attention here."

"Fine," Rodney crossed his arms over his chest belligerently. "Say what you need to say."

"If it looks like I'm not gonna make it out of this get General O'Neill down here," Sheppard ordered. "His gene should be strong enough to let him step in and start a new maintenance cycle if it's needed. I spoke to Atlantis before she got damaged and got her agreement to let O'Neill communicate with her directly. That device might be screwing up all the files but it _did_ work as advertised, so you know, just on the off chance Atlantis _does_ recover during this and I'm out of the equation, she won't stand in O'Neill's way like she must have in the future. It's not much of a backup plan but ... it's all we've got."

"Oh," Rodney's eyebrows shot up in surprise. "That wasn't what I was expecting."

"If I can I'm gonna try to do the most crucial files first," Sheppard explained. "That way, we can still gain something from anything I can fix." Sheppard held Rodney's gaze intently. "You have to be ready to get the General into the Chair asap if it proves necessary – we can't afford to give the Replicator programs time to gain back any ground. Just ... regardless of whether I finish the cycle or not I'm trusting you to know when to start the shutdown."

"Understood," Rodney's face fell as he realised two things - firstly there was no way he was gonna spare Sheppard this one and secondly John was planning something and counting on him to work out what it was when the time came ... at the risk of Sheppard's life. But no pressure!

"You've been a good friend Rodney," Sheppard dropped that one in unexpectedly. "You too Carson. Tell the others I said sorry. Until I get out of this thing Major Lorne is in charge." Before Rodney could respond Sheppard sat down and activated the Chair systems, closing his eyes as he relaxed back into the reclined position.

"Wait, you're doing this right now?" Rodney protested, pacing back and forth in front of the chair in agitation. "_Sheppard!_" But John was already inside the maintenance subroutine, no longer aware of what was going on in the real world. "I am so dead," Rodney muttered to himself, already anticipating Elizabeth's reaction, not to mention Teyla and Ronon's.

"Elizabeth," Carson activated his radio to report in reluctantly. "You and General O'Neill might want to come down to the Chair Room ... Sheppard just activated the subroutine."

There was a heavy pause before Elizabeth replied. "We're on our way."


	14. How long’s this gonna take McKay?

**Chapter 14: How long's this gonna take McKay?**

Sheppard felt the tingling energy of the subroutine sucking him into the system. Opening his eyes he saw exactly what he expected ... the strange computer world that Atlantis had shown him. Glancing down at himself he realised that he had the perception of a physical presence within the systems which was kind of a relief. The idea of travelling through Atlantis as some kind of disembodied spirit would have freaked him out.

It was different from the memories he'd been a part of ... John was awash with excitement and anticipation as he perceived for the first time the power and freedom he now had access to. It was alluring ... mesmerising ... distracting. Shaking himself he refocused, looking for the guidance the subroutine was supposed to be providing him. There up ahead was the first pocket of file code flagged for his attention – it was time to begin.

oOo

"You let him do this without clearing it with me first?" Elizabeth looked at Rodney accusingly, General O'Neill standing silently beside her.

"Hey I knew nothing about this," Rodney retorted defensively. "He sat down and activated the Chair before we even knew what he intended."

"You know what John's like," Carson added, supporting Rodney's statement.

"Did you at least find a way to track his progress?" Elizabeth relented somewhat.

"Yes I did," Rodney ran a second connection from the laptop he'd hooked up, plugging it into the big display screen across from the chair. "This will show us the level of fragmentation." A simple diagram like a petrol gauge appeared, currently displaying the needle pointing on the wrong side of middle.

"Don't worry Elizabeth," O'Neill put a hand on her shoulder reassuringly. "Sheppard's got plenty of time to make this work."

"I need to organise an IV line and some monitoring equipment," Carson announced, immediately contacting his staff to bring down the necessary items.

"We probably need to run this in shifts," Rodney suggested. "Sheppard's gonna be in there for hours ... someone should remain with him but it doesn't need all of us. I'll take the first shift ... I'm sure Teyla and Ronon will want to sit with him too."

"I'll need a member of my staff present at all times as well Elizabeth," Carson added. "At the very least I can keep an eye on how he's doing physically."

"Okay Rodney, Carson," Elizabeth looked reluctant to leave with Sheppard's future, the future of the entire city, still so uncertain. "Keep me informed."

oOo

John existed completely in the strange computer world that was the systems of Atlantis. The concept of time was meaningless ... the thrill of complete mental freedom powering him through the systems more rapidly than he could have imagined. He was enervated by the experience ... removed from physical concerns like fatigue, hunger, stress, loneliness.

He kept himself on track with iron control, discovering once he'd gotten into the swing of things that he'd arrived just in time. The fragmentation was extreme ... tiny pieces of individual files scattered deliberately as wide as possible. Fixing everything was going to take some doing.

oOo

"How long's this gonna take McKay?" Ronon turned up in the Chair Room to relieve Rodney four hours later.

"Progress isn't exactly moving in a linear fashion so I really have no idea," Rodney admitted. "But based on how slowly that gauge is moving I'd say longer than any of us are gonna like." Rodney drew Ronon's attention to his monitor screen, showing that the 'petrol' gauge was still hovering near the middle.

"How's he doing?" Ronon glanced at Sheppard's still form silhouetted by the glow of the active Chair.

"Carson said he's fine," Rodney muttered, looking across at the current nurse in attendance.

"Okay, well I got it," Ronan waited for Rodney to get up so he could have the chair they'd set up next to Sheppard. "Go – get some sleep."

Rodney nodded tiredly, pausing at the doorway to glance back at John before turning and shuffling off down the corridor.

That set the scene for the hours that followed ... Ronon was replaced during the night by Teyla who sat with Sheppard until Rodney turned up again early the next morning.

"Okay, let's see where we're at," Rodney moved straight over to the monitors, his face falling when he saw there was still a long way to go. "_Oh what?!_"

"He has not made as much progress as you would have liked?" Teyla asked worriedly.

"Not so much, no," Rodney admitted weakly.

"Doctor Beckett was confident the drip would sustain John," Teyla reminded him.

"Yeah but that's not the only risk," Rodney looked over at Sheppard worriedly. "The longer he stays in there ... the more chance there is he won't be able to disconnect his mind, just like in the future."

"Colonel Sheppard is strong Rodney," Teyla said confidently. "He will not let that happen."

"Yeah well I hope you're right," Rodney tapped a few keys on his laptop before continuing, "because based on these estimates it could be as much as another two days before he can get that gauge all the way to 100 percent."

"Have faith Rodney," Teyla put a hand on his arm before taking her leave. Rodney stood looking after her, lost in thought ... shaking himself visibly he turned and took his place in the seat next to Sheppard.

oOo

Doctor Weir and General O'Neill checked in on Sheppard while Rodney was still 'on duty'.

"Progress Rodney?" Elizabeth asked, standing beside the Chair and looking down at John in concern.

"Physically he's doing great," Rodney reported. "Carson said all his stats are within the normal range."

"And mentally?" Elizabeth persisted.

"The only measure we have for that is the fact that the gauge is still moving up," Rodney admitted. "He doesn't appear to be distressed in any way and he's progressing the defragmentation – slower than I would have liked but he'd definitely achieving something in there."

"Have you made any progress in coming up with a way to disconnect him?" O'Neill asked.

"Huh?" Rodney's mouth practically gaped at that question. "How did you know I was – "

"Hello – I'm from the future, remember?" O'Neill interrupted. "The situation might be a little different but you're still you McKay ... and that's what you did the last time I saw this."

"And clearly I didn't succeed," Rodney's faced dropped in disappointment. "Is there anything I _did_ do right?!"

"You got me here," O'Neill said simply.

"Yeah, too late to stop us from plugging in that add-on," Rodney complained.

"You got me here," O'Neill repeated, "and gave Sheppard less work to do in there. It'll be the difference that makes it work this time."

"I'm glad you're so confident," Rodney said sarcastically. "You'll forgive me if I don't put my faith in that alone."

"Do what you have to," O'Neill replied, undaunted by the acerbic tongue of Rodney McKay.

"Keep me informed Rodney," Elizabeth drew their visit to a close. Rodney nodded, bending his head back over his laptop. Just because General Future said he wasn't successful wasn't reason to stop trying ... they'd already changed things, hopefully enough to make a difference in many areas. Who said he couldn't change things a little more?

oOo

Day two of the maintenance cycle drew to a close with a progress gauge still showing there was a long way to go. The rest of team Sheppard continued their chair-side vigil making sure that John was never left alone – in each of their minds the presence of a nurse didn't count.

Teyla was in attendance when one of Carson's monitors started to beep a warning. The attending nurse moved to check it out, tapping her earpiece moments later to request Doctor Beckett's presence. Teyla looked at Sheppard worriedly ... he was pale and too still when she was used to him almost in perpetual motion. She didn't like what he was doing to himself, despite her understanding of the necessity. If only she could communicate with him in some way ... unfortunately some experimentation after John had told her about his connection to the city had revealed that Wraith mental communication was incompatible with the Ancient systems.

"Good morning Teyla," Carson greeted her as he walked briskly into the room. He and the nurse held a whispered conversation before she hurried from the room. Carson moved back to check on Sheppard.

"Is something wrong Doctor?" Teyla asked, looking down at John in concern.

"Nothing to worry about lass," Carson reassured her. "The saline solution has been keeping him nicely hydrated but his blood sugar levels are starting to dip below the point I'm comfortable with. He just needs a little boost of energy so we're going to change what we're giving him."

The nurse returned with a clear bag of fluid and saw to connecting it in place of the old one.

"This is just a little sugar ... hopefully it'll be enough to keep him comfortable," Carson looked across at Teyla, frowning at the dark rings under her eyes. "You look tired lass ... it's only an hour until Rodney returns – why don't you let me sit with the Colonel until then?"

"That is very generous Carson," Teyla replied, "but I am quite content to remain until Rodney arrives. There will be plenty of time to sleep after that."

"Well if you're sure," Carson waited a moment while Teyla nodded with a gracious smile. "I'll see you later then."

"Thank you Doctor," Teyla turned back to Sheppard, concern for her friend evident on her face. She knew that John was strong, had seen him power through situations that would have felled many. And yet this was different ... she had faith in him and his abilities but perhaps not as much faith in the Ancestors as she used to. This was not the first time something of their design had turned out to be inexplicably dangerous.

"You must hurry John," she whispered, placing a hand on his arm and squeezing lightly.

oOo

And then it was day three.

Everyone was tired and worried and beginning to do a poor job of hiding it. Carson had upped the concentration of dextrose in Sheppard's IV ... he was no longer convincing anyone that he wasn't worried about John's physical condition. Sheppard was deathly pale and still ... and somehow blank, a fact that was even more worrying than his obvious physical weakness. Nothing could have said it clearer that John's mind was very far away.

Halfway through the day an impromptu meeting of Team Sheppard, Carson, Elizabeth and General O'Neill took place in the Chair Room. Everyone was worried that Sheppard had already been immersed in the maintenance cycle for too long. They could see how he was doing on the outside but had no way of knowing if that was translating to the inside and perhaps affecting his ability to continue what he'd started.

"How long was Colonel Sheppard connected in your time before he ...," Elizabeth trailed off weakly, keeping her eyes fixed on John's face. Rodney started at the question, rubbing a hand over his face tiredly as he realised that was really a question they should have asked _before_ Sheppard had sat in the Chair.

"Four days," General O'Neill admitted.

"And I'm guessing your Carson was doing everything ours is," Elizabeth commented.

"Sheppard was hooked up to the same stuff," O'Neill replied evasively.

"So we have another day before he passes the point of no return," Rodney grimly summed it up in a way they could all understand.

"The gauge is much closer to the end now," Teyla pointed out hopefully. "Surely that means John will be finished in time?"

"I'd like to say yes but his progress has been very sporadic," Rodney admitted. "I've been tracking the pattern – there have been periods where lots of files must have been defragged but then other periods where it seemed like nothing was happening at all."

"So you can't predict when he'll come out of this?" Elizabeth's expression was blank now.

"I'm sorry," Rodney felt uncomfortable with the fact that for all his PhDs, all his claims of being a genius, he still couldn't come up with a reliable estimate for something that sounded so simple.

"And there's nothing more we can do to help him physically?" Elizabeth turned to Carson hopefully, her expression falling when Carson shook his head sadly.

"It's all up to Sheppard," O'Neill said grimly.

"It always is," Rodney retorted bitterly. "Let's hope this isn't the time when it becomes too much for him."

**Authors Note:**

I'm assuming the rest of Team Sheppard would do two four hour shifts each over a 24 hour period to keep watch over John ... I have no idea if that would work in practice but let's just assume it does. Also apologies for the delay posting this chapter ... I had an internet issue today and a willpower issue last night (had to watch The Lost Tribe ... which meant I had to watch First Contact again ... and then muck around with another story ... and then it was really late ... oops). Hope this chapter was worth the wait. :D


	15. I trust him with you

**Chapter 15: I trust him with you**

Elizabeth and the General stayed for a few minutes more before Elizabeth's duty to the rest of the city and O'Neill's understanding of team dynamics drew them both from the room.

By unspoken agreement Team Sheppard began their group vigil – none of them wanting to risk not being there when John came out of it. Carson assigned himself the duty of being the attending medical person, unwilling to trust his patient to anyone else.

Rodney's description of how the file defragmentation was proceeding proved very illustrative when it seemed like nothing was happening. The progress gauge was like a visual magnet ... each person trying to resist staring at it but continually finding their eyes drawn back to it. No one spoke ... even Rodney for once having nothing to say in the face of so tense a situation.

The gauge continued to do nothing, stubbornly clinging to its position 12 percent away from completion.

And then with sudden rapid progress the gauge sped up ... 10 percent to go ... 9, 8, 7 percent and still zooming. The suspense was painful. 5 percent, 4, ... 3, ... only 2 percent to go. With a surge the gauge hit the edge – finally they were at 0 percent remaining.

"_He's finished_," Rodney reported incredulously. Teyla and Ronon exchanged relieved expressions, eager to speak with Sheppard and see for themselves that he was okay. Carson hovered over John, ready to assess his real condition once he woke up. But John didn't wake up.

The tension was back with a vengence as Sheppard remained connected to the Chair, still and silent, deathly pale and blank of everything that made him who he was.

"Why isn't he coming out of this?" Ronon demanded impatiently.

"I don't know," Rodney complained. "The way he explained it, the subroutine would release him once the cycle was complete. Unless ...," Rodney trailed off as it suddenly struck him. _This_ was what Sheppard had been alluding to when he's told Rodney he trusted him to know when to start the shutdown.

"Unless what Rodney?" Teyla's voice shook very slightly in concern.

"Unless he's gone off to search for Atlantis," Rodney finished with a sick expression. "He knows what's at stake but he just couldn't resist the 'have to save everyone' mentallity. This is so typical! He practically told me he's leaving it up to me to decide when to pull the plug."

"He's gonna get himself trapped in there," Carson paced in frustration. "Can't you do something Rodney?"

"Do what?! You heard him before he went in there," Rodney protested grimly. "We can't break the mental connection – not without killing him! I've been trying to come up with a way around that for the past three days without success. O'Neill said I couldn't do it in the future - it's a sure bet I'm not gonna do it in the next few minutes!"

"So we just sit around and wait for him, even though he could be killing himself in there?" Ronon almost growled.

"Unfortunately yes," Rodney replied dejectedly. "We need to report this to Elizabeth."

"John," Teyla put a hand to John's forehead, speaking softly. "Please hurry."

oOo

"Shut it down now," General O'Neill ordered grimly. He and Doctor Weir had rushed down to the Chair Room as soon as they'd been told all the files had been repaired.

"What?" Rodney looked at him aghast. "Sheppard's still in there – that could kill him!"

"And if the Replicator programs take hold again everyone ends up dead, him included," O'Neill countered grimly. "_Now shut it all down!_"

"NO!" Rodney retorted defiantly. "You might be General 'In Charge' where you come from but in _this_ time that's not your call."

"No - it's mine," Elizabeth confirmed sternly. "Is there any evidence the Replicator programs have begun to reinstate themselves?"

"None," Rodney said firmly. "My readings still confirm zero fragmentation."

"Yeah - for the moment," O'Neill couldn't resist adding.

"Sheppard just needs a little time to ..." Rodney trailed off miserably, not sure how to describe what they thought Sheppard was doing.

"Find his Atlantis and save her?" O'Neill said somewhat snidely. "He needs to learn that you can't save everyone."

"I've read your file General," Elizabeth looked at him pointedly. "That's hardly in line with your usual motto of not leaving anyone behind."

"Yeah well ... times have changed," O'Neill's expression was bleak. "Now I'd be happy to save even a few people ... that isn't something I was too successful at in the future."

"I'm sorry," Elizabeth was genuinely sympathetic, hardly able to imagine a future that had effected so radical an attitude adjustment on a man like Jack O'Neill. "But I agree with Rodney ... we'll give Colonel Sheppard some more time."

Rodney let out a happy cheep, accompanied by Teyla's relieved smile and the almost imperceptible relaxing of Ronon's attack stance. If Elizabeth hadn't agreed it was obvious that the rest of Team Sheppard wouldn't have backed down without a fight.

"But if there's _any_ indication that files are beginning to fragment again I want to know about it," Elizabeth looked at Rodney sternly. "_Immediately_ Rodney."

"Of course," Rodney agreed, praying silently that Sheppard would be quick.

oOo

And then it was done ... Sheppard looked around for more pockets of code flagged for repair but there weren't any. He could feel the subroutine giving him the opening to exit the system and return to himself but he turned away resolutely. He had to find Atlantis first - then he could get out of there before Rodney shut everything down and pulled the add-on.

Up until that point he'd been at the nuts and bolts level - drilled down to the smallest components of the system. If he remained with that view he'd never find Atlantis ... it was time to go skyward.

John focused on getting a top level view of the systems and felt a corresponding rush of motion. When the blur cleared and he came to a stop he looked around curiously, trying not to be distracted by the perspective that he was hovering in midair with no visible means of support. It was amazing ... he was viewing everything as if floating high above the city, the ghostly outlines now depicting buildings and walkways, corridors and rooms. It was beautiful ... shining like a diamond against the backdrop of darkness.

Luckily everything was completely recognisable as the city of Atlantis. Sheppard took a moment to get his bearings ... yes, there glowing brightly in the distance was the ZPM room. Rodney's safe zone would be close by. But where was Atlantis herself?

Moving himself a little closer he started to skim over each building, looking for anything that didn't seem to be part of the structure itself.

There!

A tiny shimmer of rainbow light flashed at the edge of his vision. He raced towards it, passing through the walls until he was walking instead of flying. As he got closer he could hear ... or maybe it was feel ... the shifting chorus of multiple notes. It was Atlantis! And then he was at the door ... a closed door that didn't open when he approached, nor when he commanded it to open.

"Atlantis," he called out strongly. "It's Sheppard. Open the door."

"I don't know you," the reply was shouted defiantly back at him.

"You _do_," Sheppard insisted. "If you open the door you'll see your city ... and me. Everything will become clear again. I promise!"

"You cannot promise what you cannot control," Atlantis refused to be swayed.

"Look, I fixed all your files okay," Sheppard said insistently. "You must have access to your systems in there because you're keeping that door locked - have a look, see for yourself I'm telling the truth."

"Why does it matter to you?" the chorus was puzzled now ... he was getting through to her.

"Because if we don't shut down all the systems immediately the Replicator program will begin separating all your files again. I need to get you to a safe zone to protect you." Sheppard hesitated before adding something else. "And because you're my ah ... you're my friend. I don't want to see you lost forever."

There was a pause during which Sheppard wondered if he'd completely blown it. And then the door opened, revealing the awareness of Atlantis. Sheppard didn't see her in the human form he'd become accustomed too but as she truly was. She dazzled his eyes, a shimmering cascade of rainbow light accompanied by jewel tones so sweet they brought a tear to his eye - well they would have if he was the sentimental type – which he wasn't. She stood before him for a few moments before her form morphed back into the Atlantis he'd seen before.

"John?" Atlantis looked at him with dawning recognition.

"Finally!" Sheppard reached out and grabbed her hand, urging her to come with him. "I'd like to stand around and chat but we need to get to the safe zone right now." Not waiting for her agreement he broke into a run, racing down the corridors towards the nearest transporter node, drawing her along behind him.

"Slow down," Atlantis commanded, stopping suddenly and bringing Sheppard to a halt along with her. "If you had let me respond before dragging me away I would have told you that all this running was not necessary. I can take us instantly to wherever we need to be."

"Oh," Sheppard said somewhat lamely. He recovered quickly though. "Great - take us to the ZPM room - McKay set up the safe zone next to it."

Before he'd completed that sentence Atlantis made everything blur and rush again ... his perception cleared and he found himself at the door of the ZPM room. Beside it was another door that wasn't there in the real Atlantis - the door Rodney had installed to close off the safe zone.

"This is it," he gestured for Atlantis to step up. The door swished open ... inside the room was empty. It wasn't what was inside it that was interesting ... it was the walls themselves. They seemed to be composed of piping crisscrossed and intertwined in intricate confusion - with no gaps and no visible way to unravel them they must be the protection Rodney had spoken of. "Rodney assured me this would sustain you during the total systems shut down."

"And you trust Doctor McKay to have set this up correctly?" Atlantis stood warily at the doorway, obviously hesitant about stepping through.

"I've trusted him with my life on more than one occasion," Sheppard replied. "And I trust him with you. How about we go in there together?" He squeezed the hand he still held, waiting for her response.

"Very well," Atlantis stepped over the threshold, Sheppard at her side. "Doctor McKay based this design on the portable storage device?" she looked at John in surprise.

"Yeah ... he's pretty fond of calling himself a genius ... but he earns it," Sheppard hesitated, not sure if anything else needed to be said. "I guess I'll talk to you when this is all over." Turning away John stopped when a thought occurred to him. "Ah ... how do I get that doorway to reappear?"

"Think it and the exit will appear," Atlantis instructed.

Sheppard tried but nothing happened. "Okay, that's not working," he glanced back at Atlantis in time to see the concerned expression. "I'm guessing that's bad."

"How long have you been contained within these systems?" Atlantis asked.

"No idea," John admitted. "It's all a bit of a blur ... a day or so?"

"It has been almost 4 days," the shock on her face as Atlantis accessed the time stamps within her own system spoke more clearly than anything else.

"Carson was going to fix up some kind of drip thing so I should be okay," John dismissed the concern much as he usually did.

"It is not just your physical self at risk from prolonged separation," Atlantis said sternly. "Your mental link to yourself has been weakened as much as your body itself, enough that you can no longer get back by yourself."

"Wait," John held up a hand that shook slightly. "Are you telling me I'm ... stuck in here?" He was used to physical peril, maybe even courted it at times, but the thought that he'd put his mental state, his very existence at risk was more than a little disturbing. And not just because he'd gone the whole mind trip thing with Aperio in the past.

"We must act quickly," Atlantis replied evasively. "You will need to give yourself over to me so that I can return you."

"Give myself over?" John repeated sickly. "No offence but that doesn't sound like something I'd want to do willingly."

"I understand your reluctance," Atlantis spoke softly. "There is something I can do to convince you that my words are true. Our connection is two way. I will give myself over to you first so that you might search for what you know of me ... you will see for yourself that you can trust me to do this for you."

John looked at Atlantis intently before nodding a silent agreement. The connection between them that was always there but never really focused on swelled in intensity and John was greeted with rapid flashes of a history so vast he could barely comprehend it. Understanding was instant ... the core of Atlantis her constancy and commitment to those living in her city. And beyond that John saw her genuine desire to see him back to himself ... her feelings of revulsion at the idea of him remaining trapped, separate but somehow also within her. And John knew with certainty ... he could trust her.

"Okay," John spoke confidently. "Do it."

"Thank you," Atlantis acknowledged his trust with a smile. "In fixing the systems you have stepped beyond the bounds of anyone I have ever known," Atlantis reached out and took both his hands in hers. "I lack the notes to express what this means to me."

"Don't worry about it," Sheppard looked down awkwardly. "Get me out of here and we'll call it even."

"I will not forget this John Sheppard," Atlantis intoned, pulling him down until his forehead rested against her own. The rainbow hue of lights shone from her eyes, dazzling him. The harmony of notes rose sharply, the light sparkled. Sheppard closed his eyes and gave himself up to her, overwhelmed as the music and colour seemed to travel through him.

**Authors Note:**

Only two chapters to go kids ... hope you enjoyed this latest installment.


	16. You can open your eyes

**Chapter 16: You can open your eyes**

"Oh thank God!" Sheppard came back to himself hearing Carson's relieved exclamation.

"Shut it down McKay," the words were out of Sheppard's mouth while he was still disorientated. He waited a second for everything inside his head to come to a standstill before opening his eyes. "Hey Doc!" he greeted Carson weakly.

In the background Rodney called up to the Control Room, warning them that he was about to shutdown the entire system.

Sheppard looked around, seeing the rest of his team also in attendance. "Guys!" He powered down the Chair, shifting himself into the upright position in the process. "Man was that a ride!" He laughed at the euphoria of success flooding through him ... that was until he tried to stand up and found that his legs were so weak he couldn't support himself, forcing him to sit down abruptly at the foot of the Chair platform.

"You've been at this for almost four days straight Colonel," Carson admonished, dropping down beside him. "We need to get you down to the infirmary and make sure you haven't done yourself any permanent damage."

"In a minute," Sheppard insisted flatly, already coming down from the mental high. Carson looked ready to argue the point and John jumped in to head him off before he could. "Please Carson," Sheppard looked at him hopefully, "I really do feel okay."

"Ten minutes," Carson offered sternly. "But if you start to feel _anything_ unusual you'll tell me immediately. If I find out you've glossed over something you'll wish you hadn't lad."

"Thanks Doc," Sheppard said gratefully. "Rodney - how's it coming?"

"Still working," Rodney said in that 'don't interrupt me' tone. He'd set up a series of programs to effect the shut down from the Chair Room but it still took time to run them in the proper sequence.

"It is good to see you John," Teyla said softly. "We feared you had remained within the systems for too long."

"I had no perception of time passing," Sheppard excused the length of his service to the maintenance subroutine. "It was all just a blur of searching, joining and transporting things the system showed me."

"Sounds interesting," Ronon grinned before adding, "much more interesting than from this side anyway. It's been pretty boring watching over you sitting in that chair for four days."

"Sorry I couldn't do anything to entertain you buddy," Sheppard quipped. He raised a shaking hand to cover eyes that weren't used to the bright light, quickly whipping it back to the floor when he noticed Teyla's narrowed look.

"Did you succeed in locating Atlantis," Teyla asked with concern.

"Yeah," Sheppard nodded. "Just as well too ... I had a little bit of trouble at the end there."

"So you helped her and then she helped you?" Ronon asked.

"Something like that," Sheppard agreed casually, not ready to talk about what he'd experienced just before exiting the system. He needed to think about it himself first, make sense of the confusion of thoughts and impressions still swirling at the back of his mind, and accept what he'd inadvertently shared of himself.

"We should let Elizabeth and General O'Neill know you have returned," Teyla said reluctantly.

"Just - let's wait until Rodney's finished before we report in," Sheppard looked at Teyla with a hint of pleading in his eyes.

"Very well," Teyla acknowledged his request. "Perhaps we should get you off the floor while we wait."

"I'm okay down here," Sheppard resisted their attempts to pull him up, preferring to remain where he was while Rodney did his thing. He's sat in the Control Chair enough to last him the rest of his life ... the floor was a welcome change.

The city shut down one sector at a time, sweeping a wave of darkness across Atlantis. The emergency lighting took over, casting the Chair Room with an eerie glow.

Rodney walked over to the back of the Chair, and reached down. There was an audible click of two components separating before Rodney rose, Replicator enhanced data pad held triumphantly aloft. "What do you know - it worked!"

A few key strokes later the systems were slowly coming back on line. It took a while, enough that John was really beginning to struggle with staying awake, before Rodney finally made a happy sound and announced that everything was up and running again.

"Nice work Rodney," Sheppard didn't let himself relax just yet ... there was still one thing he needed to do. He'd done enough mental activity to last him a long time - his brain actually felt tired, along with the rest of him. "Atlantis?" he spoke aloud, not caring the others wouldn't be able to hear the other side of the conversation he hoped he was about to have.

"_John Sheppard_," the gentle tones of Atlantis greeted him as they'd always done.

"You're back!" Sheppard looked at the others with an openly happy expression.

"_Thank Doctor McKay for his efforts_," Atlantis intoned. "_The safe zone held with ease - his design was truly remarkable_."

"She said thank you Rodney - your design worked as advertised," Sheppard passed on, amused when Rodney almost blushed at the compliment.

"Times up," Carson had been standing silently in the background monitoring John's readings discretely. Now he stepped up insistently. "The device has been removed, all the files have been fixed and Atlantis is back to being herself again. It's time to get you down to the infirmary Colonel."

"Okay," Sheppard rested his head against the base of the Chair tiredly. "Just give me a moment and I'll walk down there with you."

"You bloody well won't," Carson retorted, losing his patience with John's stubbornness. "I'm calling for a gurney right now and I don't want to hear any arguments from you."

"But -" Sheppard broke off as Atlantis hummed disapprovingly.

"_It is time to rest John Sheppard_," she insisted, washing his mind with the range of her notes as before. He felt himself drift off, asleep before Carson could even tap his earpiece. Just before Sheppard dropped off he made a note to himself to have a word with Atlantis about the whole musical sleeping pill thing.

"Stubborn fool," Carson looked down at Sheppard in fond exasperation.

It didn't take long for the medical team to arrive and set Sheppard up for transport. With Carson wheeling his equipment and Rodney, Ronon, and Teyla trailing along behind them, the procession travelled the corridors of Atlantis, their exhausted friend's soft snores accompanying them.

oOo

It was his rumbling stomach that woke Sheppard up hours later. Before he'd even opened his eyes he knew he was in the infirmary ... _again_ ... and that at least one member of his team was in attendance.

"You can open your eyes," Rodney said irritably. "We know you're awake - no one could sleep through the noise your stomach's been making."

"Yeah, well when you haven't eaten for a week you get a little hungry," Sheppard rubbed a hand over his face, noting the thick beard that would have to go at the earliest opportunity. He'd expected one person to be sitting with him but in fact he had three. "Don't you guys have somewhere else to be?"

"We all wished to speak with you when you awoke," Teyla said graciously. "It has been a ... _difficult_ few days."

"Sorry about that," Sheppard knew how hard it would have been to sit around and do nothing. He wasn't sure he'd be able to handle that if he'd been in their place. And then there was the fact that he'd jumped into the Chair without telling them first ... he knew he'd be in for some form of retribution for that, and that he probably deserved it - he just hoped they'd hold off until after he felt stronger. "What's been happening here while I was ah ..." Sheppard trailed off, not sure now how best to describe his experience.

"Communing with the city?" Rodney smirked at John's uncomfortable expression. "You should have heard some of the rumours doing the rounds ... your mystery status has gone up a few points and it was already pretty high."

"I hope you squelched the rumours without giving anything away," Sheppard looked at Rodney pointedly.

"Of course," Rodney waved a hand expansively. "Told them the truth pretty much - that you were running a deep level routine to help repair the systems damage - and that it was taking a long time because there was a lot of damage."

"Oh," Sheppard nodded thoughtfully, happy with that.

"Doctor Weir and General O'Neill both stopped in to see you a short time ago," Teyla continued. "They will be keen to speak with you now that you are awake."

Before Sheppard could respond to that his stomach rumbled again ... loudly.

"I will see about getting you something to eat," Teyla rose, putting a hand on Sheppard's arm before walking away.

"Glad you're back buddy," Ronon slapped Sheppard's shoulder in manly affection before following Teyla from the room.

"So we really are in the clear now the add-on's been removed?" Sheppard turned back to Rodney with that query.

"I've got Radek running every diagnostic we've got at our disposal," Rodney replied. "So far it's all in the green. What about you ... you didn't do something permanent to that brain of yours while you were in there did you?"

"I'm all there Rodney," Sheppard smiled in amusement. "You know it was pretty disturbing being disconnected from everything physical but at the same time it was kinda cool. Everything was super responsive and super fast ... I can see how that would have been enough to lure some of the Ancients into sticking around."

"Unlimited mental freedom?" Rodney echoed how Atlantis had described it. When Sheppard nodded wordlessly Rodney shrugged. "Not much good if you're stuck inside a system – your experience with Aperio would have taught you that."

"It's the first time what happened with Aperio has come in handy," Sheppard joked.

"Yes well we're all glad you decided to stick to being an ordinary physical person," Rodney said somewhat snidely.

"Try and tone down your relief McKay," Sheppard said blandly.

"Maybe I'm just getting blasé about you risking your life," Rodney retorted. "This isn't exactly our first bedside vigil you know."

"_Rodney_," Teyla admonished, walking back to Sheppard with a tray ... the boring, just recovering from days without food kind. "Rodney was just as relieved as the rest of us that you completed the repairs without injury," she told him.

"In any case, the only thing left to finish off this unpleasant episode is to return General O'Neill to his own time," Rodney changed the subject before Sheppard could call him up on it.

"Do we know how to do that?" Sheppard looked at Rodney expectantly.

"It's all on that laptop he brought with him," Rodney explained. "We just have to connect and run the automated procedures through the Containment Lab systems."

"How confident are -," Sheppard began, only to be interrupted by Teyla.

"We should let you eat in peace," she said firmly in a tone that said 'don't argue'. "I am sure Rodney has work to do to prepare for the General's departure. He can fill you in later."

Sheppard smiled tiredly as Teyla and Rodney took their leave, Teyla urging Rodney to move when he'd clearly wanted to hang around. Sheppard then focussed on doing everything he needed to so Carson would release him from the infirmary sooner rather than later.

oOo

Two days after he'd come out of the subroutine Sheppard sat in the infirmary, waiting impatiently for a full medical check ... if Carson was happy with the results John would get his freedom.

"You've managed to come through this surprisingly well Colonel," Carson reported once he'd finished. "You'll need to make sure you eat regularly and more often than usual until you've gained back the weight you lost, get as much sleep as possible ... in a week you'll be as good as new."

"Thanks Doc," Sheppard looked at Carson hopefully. "Does that mean I can get out of here?"

"Go," Carson replied, stepping aside so John could see the clothes he'd set aside for him. "And this time, try and stay out of trouble."

"I always try," Sheppard quipped, "I'm just not always successful!" Before Carson could say anything else Sheppard jumped off the bed, grabbed the clothes and went to put them on in privacy.

**Authors Note:**

I have no idea how long it would take to be up and about after 4 days of inactivity and no real food ... it's Shep though and his recovery skills have always been amazing so two days seemed about right ;D

Sorry editing of this took a bit longer than I expected ... I'm still not happy with some of it but there you go. Enjoy!


	17. It’s really only a matter of time

**Chapter 17: It's really only a matter of time**

Sheppard headed straight for his quarters from the infirmary ... he was due for a debrief with General O'Neill and Elizabeth upon his release but didn't think they'd begrudge him some time to get things in order first.

Looking at himself in the mirror for the first time since he'd sat in the Chair was a real eye opener – even after two days he looked gaunt, pale and somewhat piratical with the thick beard he was sporting. His eyes were red rimmed and he _still_ looked like he hadn't slept in a week – except for his hair which looked like he'd been rubbing his head into his pillow for days. "I look like crap," he muttered under his breath.

Okay, first things first. Sheppard went to work on getting himself back to clean shaven ... well, as good as it got for him ... feeling more like himself as soon as the beard was gone. He showered, changed into his own clothes, and then decided he'd stalled enough.

"You okay?" he directed the question into the air, seeking out the presence of Atlantis.

"_We are adjusting_," Atlantis chorused a reply. "_It will take time to reacquaint ourselves with all our systems_."

"As long as you're good," Sheppard said casually, hesitating before continuing. "I gotta admit that ... sharing thing we did at the end there has me feeling a little ..." he trailed off, not really sure how to describe his current feelings.

"_Exposed? Uncomfortable? Confused?_" Atlantis suggested just as casually. "_It was to be expected. This is why we have left you to silence during your recovery_."

"Oh," Sheppard raised an eyebrow in surprise. "Listen, I was thinking about what you revealed when the connection was going in my direction," he persisted. "It was glimpses of your past wasn't it?"

"_Our past, our feelings, the essential core that makes us who we are_," Atlantis agreed. "_We tried not to overwhelm you with more than your mind could handle but even so it must be difficult for you to process the information you received_."

"I don't think I can," Sheppard admitted. "It all happened really fast and to be honest I was already kinda tired. Most of it's already faded but what I do recall doesn't change my opinion about you."

"_Thank you_," Atlantis acknowledged the implied compliment in that. "_We know you are worried about what you revealed before we used our connection to send you from the system_."

"Hey I've always been an open book," Sheppard quipped. "Clowns, Ferris Wheels, Johnny Cash. It's all there for anyone who wants to read it."

"_You are much more than the surface you let people see_," Atlantis admonished. "_But rest assured John Sheppard ... we too saw only that which supports our knowledge of you_."

"So no glimpses of anything classified then?" Sheppard kept the facade going even though he knew Atlantis saw right through him. "Cause you know if you did I'd have to kill you."

"_You are entirely too fond of this juvenile behaviour_," the chorus shifted notes in disapproval, reminding him once again of his Grandmother.

"I know," Sheppard grinned unrepentant as he headed for the door. "I'm glad you're feeling more like yourself. Just ... you know, let me know if you suspect anything isn't as it should be."

"_You were very brave_," Atlantis intoned softly before Sheppard could leave. "_Especially after we had shown you the risks of remaining connected for too long_."

"Like I said to McKay, it was strange but not unpleasant," Sheppard admitted. "Enough that knowing others chose to stay connected doesn't surprise me, although you know ... I'd never want that for myself."

"_They made us what we are_," Atlantis admitted.

"Huh?" Sheppard frowned in confusion.

"_Our awareness was not always as defined as it is now_," Atlantis explained. "_In the early days when the city was first built, before we had experienced deep mental connections with your ancestors, we were little more than the summation of our systems. You recall we said the ones who perished during the deep maintenance cycle left some of their essence, their memories, a small part of who they were behind?"_

"I do,"Sheppard nodded.

"_Each time this occurred it added to our awareness until we began to achieve individuality ... perceiving our systems as separate parts of the whole_," the chorus shifted notes discordantly before smoothing out into the wealth of combined sound Sheppard had come to expect._ "Eventually the harmony was born and we were able to converse with those strong enough in the required genes to achieve it. Often it was these very same individuals who ran the maintenance cycle when required._"

"So without the others sacrificing themselves we wouldn't be having this conversation?" Sheppard asked in amazement.

"_That is correct_," Atlantis agreed. "_It was a circular effect – the first being trapped by accident and lending themselves to our creation which in turned encouraged others to voluntarily remain connected in order to commune with us. There were those not strong minded enough to resist the allure of what they perceived as freedom but also those who genuinely believed they could attain mental independence without loss of life._"

"They wanted the full connection didn't they?" Sheppard felt a flash of sudden clarity. "Like what we did at the end - they wanted to know everything, experience time itself."

"_Not at first_," Atlantis replied, "_but over millennia, as we accumulated experiences and knowledge and history it became an ambition for some. There was nothing we could do to dissuade them because control of the maintenance cycle was locked away even from us. We could not prevent them from entering the systems and those who successfully completed the cycle, the ones capable of talking with us, ignored all our warnings."_

"Wow," Sheppard whistled softly. "That really must have frustrated the hell out of you."

"_Indeed_," Atlantis agreed. "_We were heartened when the Ancients decided to pursue other means to reverse fragmentation. The incident Doctor McKay spoke of drove them to do this but it was in our interests too. We no longer desired to let anyone have free reign within our systems._"

"What happened?" Sheppard asked grimly, already suspecting he wasn't going to like what he heard.

"_One of those capable of communicating with us saw the deep maintenance cycle as an opportunity to do more than just fix the systems or commune with our awareness_," the chorus held notes Sheppard had not heard before ... censure of a persons actions as well as anger and betrayal. "_His name was Vendius - he was young but confident beyond his years. __He lured us with false words and pretty phrases into an isolation we could not escape from and then used our absence to take over all the systems from within. It was only the demise of his physical form that released us and allowed control to be returned to the others_. _Vendius thought to survive purely within the systems long enough to convince us to give ourselves over to him and thereby teach him about existence itself._"

"He wanted you to teach him how to _ascend_?" Sheppard summarised what he'd heard down to that final point.

"_We believe so_," Atlantis agreed. "_He knew that we had witnessed many of his ancestors achieving that state. Rather than do the work himself he desired to find a short cut. We taught him nothing beyond his inability to survive without the physical form he sought to shed. But in return, he taught us much about deception, betrayal, and hidden motivations._"

"I'm sorry," Sheppard said softly. "We always kind of assumed the Ancients had risen above all that petty self motivation stuff ... even though we've seen enough to already know that wasn't the case."

"_The connection we share is special John Sheppard_, _even beyond what you know,_" Atlantis revealed. _"There were times in the past, before your Ancestors abandoned the city, when we could have conversed like this but chose not to ... until you came_."

"You hadn't spoken to anyone since Vendius?" Sheppard asked incredulously. "Didn't the Ancients try to talk to you?"

"_They did for a short time_," Atlantis agreed, "_but we did not respond. Trust had been broken and we were ... fearful of their intentions. I believe they were also fearful of us, our reactions ... perhaps explaining why they did not continue their work on expanding the Control Chair capability. After Vendius they began the project on Kallus, hoping to take away the need for such a deep connection to the systems_."

"They didn't want there to be any chance it could happen again," Sheppard nodded in understanding, realising how much was explained by that one incident. "If you want we could still get Rodney to work on automating things like the Ancients intended," he suggested.

"_We would like that_," Atlantis agreed, her chorus ringing happily at the offer. "_We are glad to see you are undamaged by the experience._"

"Good as new in a couple of days," Sheppard quipped. "Listen, I need to debrief Elizabeth and General O'Neill now – anything you want me to pass on?"

"_Just our thanks for your commitment to the city_," Atlantis offered, "_and our commitment to you and your people in return_."

"Elizabeth will like that," Sheppard said with a smile, turning and heading out to make that report.

oOo

The next day, reports made and business slowly returning to normal, Sheppard met with Elizabeth, Rodney and of course General O'Neill in the Containment Lab.

"Back where it all started," Sheppard quipped. Turning to Rodney with a raised brow he asked "All set?"

"Let me just load up the last return sequence ... okay, we're good to go," Rodney pronounced.

"I'm disappointed I didn't get to meet this awareness of Atlantis you're so fond of," O'Neill said with real regret.

"She would have enjoyed meeting you too Sir," Sheppard replied. "Maybe next time."

"Very funny," O'Neill's eyes twinkled at John's attempted humour. "It's been a blast, luckily not literally."

Rodney had filled John in on how the General had wanted to shut everything down while he was still connected. Sheppard didn't hold any resentment though – he was pretty sure he'd sacrifice more than he'd be comfortable admitting to if he knew it could save his friends, even more if it was a matter of bringing them back from the dead. O'Neill hadn't said as much but Sheppard was convinced that only the loss of someone very close explained the changes they'd noticed in the General's attitude, and his willingness to come here in an attempt to fix things.

"Tell Sam I said Hi," Rodney requested.

"I will not," O'Neill said sternly. "You know she still hasn't – "

"_Don't_ tell me," Rodney interrupted quickly. "Leave me at least some of my illusions about the future."

"O-kay," O'Neill drawled, clearly not wanting to think about what illusions Rodney might have that involved his Sam. Looking around at everyone he smiled. "Okay kids – I guess it's show time."

"Aren't you the least bit worried about what you're returning to?" Rodney couldn't help but ask.

"Nah," O'Neill replied casually. "You fixed things so with any luck I should be waking up in the future with a whole different past where I won't remember any of this. I don't want to think about it too much beyond that 'cause it will only make my brain hurt." O'Neill glanced across at Rodney with a stern expression. "I wouldn't recommend using what your future self created to power the city McKay."

"I wasn't –," Rodney began before giving in. "Fine. Are we ready to activate this thing?"

"I'm good to go," O'Neill agreed, giving no indicators that he was even bothered about being returned only he knew how many years into the future.

"Well in that case good luck General," Elizabeth said graciously. "Thank you for making the journey back here – you saved us from a future I don't even want to contemplate."

"Hey, you saved our butts just as much as we saved yours," O'Neill denied the need for thanks. He paused as if wanting to say more before turning away with a frown. "Sheppard – look after the city. I want to find it in one piece when I get back."

"Of course Sir," Sheppard smiled at the easy order.

"Hit it McKay," O'Neill waited as Rodney activated the return program on the laptop from the future. The panels that had remained active the whole time the General had been on Atlantis suddenly pulsed more rapidly.

"Better get in there," Rodney advised. "It's not going to take long for the power to build up to the required level."

"It's been an honour General," Sheppard held out a hand.

"Likewise Colonel," O'Neill shook the proffered hand firmly.

"Take care Jack," Elizabeth stepped forward and hugged O'Neill quickly.

"You too," O'Neill said softly, before turning resolutely towards the chamber. Although he wasn't a young man he still possessed more than enough flexibility to squeeze himself into the tight space. "Oh and Elizabeth?" O'Neill's tone suggested he'd forgotten to tell her something of little consequence.

Elizabeth looked to him with a raised brow.

"If there ever comes a time when McKay and Sheppard make this city fly ... stay away from the windows." Sheppard deserved something in return for what he'd done for O'Neill's future. Jack knew of other losses but he thought this was the one that would hit John the hardest, the one easiest to influence with just a few words ... and perhaps the one closest to his own heart.

Before Elizabeth could react O'Neill had pulled closed the chamber door.

"When you're ready Rodney," Elizabeth ordered, staring into the chamber at the General staring back.

Rodney activated the time travel routine created by his future self. There was a bright flash of light, the generators gave one final energy pulse, and then all was silent.

"What was _that_ all about?" Sheppard looked across at Elizabeth with a worried look.

"I have no idea," she replied distractedly.

oOo

There was nothing left to do but return to the usual routines, although understandably no one was keen to go out on any Ancient artefact hunts. Rodney had been like a kid in a candy store over the laptop General O'Neill had left behind. Sheppard was just waiting for some kind of announcement that Rodney had cracked the ultimate in power generation. In fact that's what he was expecting to hear when he saw Rodney striding into the commissary with the future laptop in hand.

"Oh I'm _good_," Rodney slumped down in the seat across from Sheppard, his look both smug and annoyed.

"How so?" Sheppard asked, glancing down at the laptop Rodney had practically thrown on the table between them..

"Because the future me booby trapped this thing," Rodney tapped a finger on the screen. "I can't access the files that run the program to activate the Containment Chamber and I can't copy them anywhere else ... not without destroying them. I should have known there was a reason O'Neill wasn't fussed about not being able to take it back with him!"

"Probably for the best McKay," Sheppard slapped him on the arm bracingly. "I don't think the world's ready for controlled time travel just yet."

"Easy for you to say," Rodney said irritably. "And don't think I've forgiven you for activating the Chair without telling me first," he changed the subject abruptly. "You scared the crap out of me ... not to mention leaving me holding the bag when Elizabeth and General O'Neill turned up."

"I wondered when you were gonna bring that up," Sheppard replied.

"I've been saving it up," Rodney retorted sarcastically. "There's no fun in kicking someone when they're already down."

"That's nice of you McKay. Look, from what I hear you handled it perfectly," Sheppard said casually. When Rodney continued to frown in annoyance John relented somewhat. "I knew you were worried about what was gonna happen ... hesitating was only making it worse for everyone. At least my way you didn't have too much time to expect the worst."

"You mean apart from the four days where we couldn't communicate with you?" Rodney retorted.

"Apart from those," Sheppard agreed. "There was no other solution Rodney – even your future self knew that. You're just gonna have to put this one away now."

"Fine," Rodney said ungraciously. "I just wish I could be around when the Replicators find out their big plan failed."

"Not me," Sheppard denied. "I've had more than enough of the Replicators for now ... it'll be soon enough to be seeing them when they launch their next attack."

"You think they will?" Rodney looked at Sheppard worriedly.

"Without a doubt McKay," Sheppard said seriously. "It's really only a matter of time."

"Time," Rodney muttered. "I think I've had enough of thinking about _time_ right now too."

"We'll handle it," Sheppard said confidently. "After all, you're still a genius and Atlantis is still around to give us that edge."

"You're right," Rodney bucked up, straightening in his chair with renewed purpose. "I think I'll just give this laptop one more go ... _I_ booby trapped it so that means _I_ really should be able to crack it."

"You do that," Sheppard drawled, pretty confident Rodney would be getting no help from the future. Leaning back in his seat he crossed his ankles and took the time to look around fondly. It was good to have the city back in full working order.

Atlantis also felt the joy in being back where she belonged. The fear discovered in losing her identity, the reminders of past events it had evoked would not soon depart ... the only thing reassuring her was the presence of John Sheppard. He hadn't left her in the dark and she knew with complete certainty that he never would. It _was_ good to be back.

**The End.**

**Authors Notes:**

As usual anything I couldn't dredge from the recesses of my own mind I researched on Wikipedia – that includes information about file fragmentation and defragmentation, and saline/dextrose IV lines.

My brain hurts when I try to work out the implications of time travel ... I think O'Neill wouldn't remember anything because the future where he had to go to Atlantis because of the add-on doesn't happen anymore. Everyone on Atlantis would remember he was there though - a nice story to tell him the next time he visits! Technically that means the laptop Rodney has from the future shouldn't exist either but rather than just have it magically disappear (cause then I would have to make O'Neill just disappear too for consistency!) I decided it was an object existing 'out of time', and so still there. Hope that makes sense!

Just have to add after the first review for this chapter that I had no intentions of 'Sparky'ing anything when O'Neill decided to warn Elizabeth. I was thinking about nothing more than friendship and leadership and how much Shep suffered because of having to leave Elizabeth behind ... not that one little obscure warning is necessarily going to succeed in changing that.

I usually try to make my Ancient names of Latin origin with meanings etc but for this one the incidental names are all just complete fabrications – they were all only minor parts and I didn't want to waste a good Latin name on them! Except for the villan of the past, Vendius. His name is based on the latin word Vendo which means, predictably, betray.

You may have noticed the other two titles in this series are also song titles ... They're a long way from being song fics but I did very loosely link the stories to the subjects for those songs. This one is the same ... it's Time After Time by The Electric Light Orchestra though, not the Cindy Lauper one. I got _some_ inspiration from the words ... it's a pretty tenuous connection but it is there.

Thank you to everyone for sticking with this trilogy ... hope you enjoyed reading it as much as I enjoyed writing it. Extra special thank you to my faithful reviewers ... I looked forward to your comments after each chapter and you never disappointed.

And lastly, what's one of the signs you're obsessed with Stargate Atlantis? When you've written over 500,000 words of fanfiction devoted to your favourite characters and don't see that as a problem! For those interested I have started work on Fortunate Journey Season 4 ... it's slow going at the moment but I am committed to writing it. Beyond that it'll be whatever comes into my head ... I like suggestions though so if you've got one PM me. Oh, and check in at my profile page because I'll update it with writing progress/plans on a regular basis.

I'm done babbling now ... TTFN


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